diff --git a/src/CMakeLists.txt b/CMakeLists.txt
similarity index 91%
rename from src/CMakeLists.txt
rename to CMakeLists.txt
index 12f408618..f004c28e9 100644
--- a/src/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -169,29 +169,29 @@ endif()
 
 # Only initialize git submodules if it is not there. User is responsible
 # for future updates of fox xml submodule.
-if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/xml/fox/.git)
-  if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
+if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src/xml/fox/.git)
+  if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git)
     message("-- Cloning FoX XML git repository...")
     execute_process(COMMAND git clone https://github.com/mit-crpg/fox.git src/xml/fox
-      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/..)
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
     execute_process(COMMAND git checkout bdc852f4f43d969fb1b179cba79295c1e095a455
-      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/xml/fox)
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/src/xml/fox)
   else()
     message("-- Initializing/Updating FoX XML submodule...")
     execute_process(COMMAND git submodule init
-      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/..)
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
     execute_process(COMMAND git submodule update
-      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/..)
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
   endif()
 endif()
-add_subdirectory(xml/fox)
+add_subdirectory(src/xml/fox)
 
 #===============================================================================
 # Build OpenMC executable
 #===============================================================================
 
 set(program "openmc")
-file(GLOB source *.F90 xml/openmc_fox.F90)
+file(GLOB source src/*.F90 src/xml/openmc_fox.F90)
 add_executable(${program} ${source})
 target_link_libraries(${program} ${libraries} fox_dom)
 set_target_properties(${program} PROPERTIES
@@ -203,28 +203,16 @@ set_target_properties(${program} PROPERTIES
 #===============================================================================
 
 install(TARGETS ${program} RUNTIME DESTINATION bin)
-install(PROGRAMS utils/plot_mesh_tally.py
-  DESTINATION bin
-  RENAME plot_mesh_tally)
-install(PROGRAMS utils/statepoint_histogram.py
-  DESTINATION bin
-  RENAME statepoint_histogram)
-install(PROGRAMS utils/update_inputs.py
-  DESTINATION bin
-  RENAME update_inputs)
-install(PROGRAMS utils/xml_validate.py
-  DESTINATION bin
-  RENAME xml_validate)
 install(DIRECTORY relaxng DESTINATION share)
-install(FILES ../man/man1/openmc.1 DESTINATION share/man/man1)
-install(FILES ../LICENSE DESTINATION "share/doc/${program}/copyright")
+install(FILES man/man1/openmc.1 DESTINATION share/man/man1)
+install(FILES LICENSE DESTINATION "share/doc/${program}/copyright")
 
 find_package(PythonInterp)
 if(PYTHONINTERP_FOUND)
   install(CODE "execute_process(
                   COMMAND ${PYTHON_EXECUTABLE} setup.py install
                   --prefix=${CMAKE_INSTALL_PREFIX}
-                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/utils)")
+                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})")
 endif()
 
 #===============================================================================
@@ -235,7 +223,7 @@ endif()
 include(CTest)
 
 # Get a list of all the tests to run
-file(GLOB_RECURSE TESTS ${CMAKE_CURRENT_SOURCE_DIR}/../tests/test_*.py)
+file(GLOB_RECURSE TESTS ${CMAKE_CURRENT_SOURCE_DIR}/tests/test_*.py)
 
 # Check for MEM_CHECK and COVERAGE variables
 if (DEFINED ENV{MEM_CHECK})
diff --git a/src/Makefile b/Makefile
similarity index 100%
rename from src/Makefile
rename to Makefile
diff --git a/docs/source/quickinstall.rst b/docs/source/quickinstall.rst
index 1ffebbebe..b64dfebda 100644
--- a/docs/source/quickinstall.rst
+++ b/docs/source/quickinstall.rst
@@ -43,8 +43,7 @@ the following commands in a terminal:
     git clone https://github.com/mit-crpg/openmc.git
     cd openmc
     git checkout -b master origin/master
-    mkdir src/build
-    cd src/build
+    mkdir build && cd build
     cmake ..
     make
     sudo make install
diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst
index d06806d98..707355ddc 100644
--- a/docs/source/usersguide/install.rst
+++ b/docs/source/usersguide/install.rst
@@ -112,7 +112,7 @@ repository::
 By default, the cloned repository will be set to the development branch. To
 switch to the source of the latest stable release, run the following commands::
 
-    cd openmc/src
+    cd openmc
     git checkout master
 
 .. _GitHub: https://github.com/mit-crpg/openmc
@@ -132,14 +132,13 @@ following
 
 .. code-block:: sh
 
-    mkdir src/build
-    cd src/build
+    mkdir build && cd build
     cmake ..
     make
 
 Note that first a build directory is created as a subdirectory of the source
-directory. The Makefile in ``src/`` will automatically perform an out-of-source
-build with default options.
+directory. The Makefile in the top-level directory will automatically perform an
+out-of-source build with default options.
 
 CMakeLists.txt Options
 ++++++++++++++++++++++
@@ -166,7 +165,7 @@ should be used:
 
 .. code-block:: sh
 
-    cmake -Ddebug=on /path/to/src
+    cmake -Ddebug=on /path/to/openmc
 
 Compiling with MPI
 ++++++++++++++++++
@@ -177,14 +176,14 @@ the MPI Fortran wrapper. For example, in a bash shell:
 .. code-block:: sh
 
     export FC=mpif90
-    cmake /path/to/src
+    cmake /path/to/openmc
 
 Note that in many shells, an environment variable can be set for a single
 command, i.e.
 
 .. code-block:: sh
 
-    FC=mpif90 cmake /path/to/src
+    FC=mpif90 cmake /path/to/openmc
 
 Compiling with HDF5
 +++++++++++++++++++
@@ -195,14 +194,14 @@ the HDF5 Fortran wrapper. For example, in a bash shell:
 .. code-block:: sh
 
     export FC=h5fc
-    cmake /path/to/src
+    cmake /path/to/openmc
 
 As noted above, an environment variable can typically be set for a single
 command, i.e.
 
 .. code-block:: sh
 
-    FC=h5fc cmake /path/to/src
+    FC=h5fc cmake /path/to/openmc
 
 To compile with support for both MPI and HDF5, use the parallel HDF5 wrapper
 ``h5pfc`` instead. Note that this requires that your HDF5 installation be
@@ -216,8 +215,7 @@ the root directory of the source code:
 
 .. code-block:: sh
 
-    mkdir src/build
-    cd src/build
+    mkdir build && cd build
     cmake ..
     make
     make install
@@ -267,7 +265,8 @@ the source code root directory:
 
 .. code-block:: sh
 
-    cd src
+    mkdir build && cd build
+    cmake ..
     make
 
 This will build an executable named ``openmc``.
@@ -293,7 +292,6 @@ in the root directory of the OpenMC distribution:
 
 .. code-block:: sh
 
-    cd src
     make
 
 This will build an executable named ``openmc``.
@@ -312,7 +310,6 @@ the source directory and run the following:
 
 .. code-block:: sh
 
-    cd src
     make test
 
 If you want more options for testing you can use ctest_ command. For example,
@@ -320,7 +317,7 @@ if we wanted to run only the plot tests with 4 processors, we run:
 
 .. code-block:: sh
 
-    cd src/build
+    cd build
     ctest -j 4 -R plot
 
 If you want to run the full test suite with different build options please
@@ -370,7 +367,7 @@ the following steps must be taken:
 
    .. code-block:: sh
 
-       openmc/src/utils/convert_xsdir.py xsdir31 cross_sections.xml
+       openmc/scripts/convert_xsdir.py xsdir31 cross_sections.xml
 
 3. In the converted ``cross_sections.xml`` file, change the contents of the
    <directory> element to the absolute path of the directory containing the
@@ -416,9 +413,8 @@ Running OpenMC
 Once you have a model built (see :ref:`usersguide_input`), you can either run
 the openmc executable directly from the directory containing your XML input
 files, or you can specify as a command-line argument the directory containing
-the XML input files. For example, if the path of your OpenMC executable is
-``/home/username/openmc/src/openmc`` and your XML input files are in the
-directory ``/home/username/somemodel/``, one way to run the simulation would be:
+the XML input files. For example, if your XML input files are in the directory
+``/home/username/somemodel/``, one way to run the simulation would be:
 
 .. code-block:: sh
 
diff --git a/src/utils/openmc/__init__.py b/openmc/__init__.py
similarity index 100%
rename from src/utils/openmc/__init__.py
rename to openmc/__init__.py
diff --git a/src/utils/openmc/checkvalue.py b/openmc/checkvalue.py
similarity index 100%
rename from src/utils/openmc/checkvalue.py
rename to openmc/checkvalue.py
diff --git a/src/utils/openmc/clean_xml.py b/openmc/clean_xml.py
similarity index 100%
rename from src/utils/openmc/clean_xml.py
rename to openmc/clean_xml.py
diff --git a/src/utils/openmc/cmfd.py b/openmc/cmfd.py
similarity index 100%
rename from src/utils/openmc/cmfd.py
rename to openmc/cmfd.py
diff --git a/src/utils/openmc/constants.py b/openmc/constants.py
similarity index 100%
rename from src/utils/openmc/constants.py
rename to openmc/constants.py
diff --git a/src/utils/openmc/element.py b/openmc/element.py
similarity index 100%
rename from src/utils/openmc/element.py
rename to openmc/element.py
diff --git a/src/utils/openmc/executor.py b/openmc/executor.py
similarity index 100%
rename from src/utils/openmc/executor.py
rename to openmc/executor.py
diff --git a/src/utils/openmc/filter.py b/openmc/filter.py
similarity index 100%
rename from src/utils/openmc/filter.py
rename to openmc/filter.py
diff --git a/src/utils/openmc/geometry.py b/openmc/geometry.py
similarity index 100%
rename from src/utils/openmc/geometry.py
rename to openmc/geometry.py
diff --git a/src/utils/openmc/material.py b/openmc/material.py
similarity index 100%
rename from src/utils/openmc/material.py
rename to openmc/material.py
diff --git a/src/utils/openmc/mesh.py b/openmc/mesh.py
similarity index 100%
rename from src/utils/openmc/mesh.py
rename to openmc/mesh.py
diff --git a/src/utils/openmc/nuclide.py b/openmc/nuclide.py
similarity index 100%
rename from src/utils/openmc/nuclide.py
rename to openmc/nuclide.py
diff --git a/src/utils/openmc/opencg_compatible.py b/openmc/opencg_compatible.py
similarity index 100%
rename from src/utils/openmc/opencg_compatible.py
rename to openmc/opencg_compatible.py
diff --git a/src/utils/openmc/particle_restart.py b/openmc/particle_restart.py
similarity index 100%
rename from src/utils/openmc/particle_restart.py
rename to openmc/particle_restart.py
diff --git a/src/utils/openmc/plots.py b/openmc/plots.py
similarity index 100%
rename from src/utils/openmc/plots.py
rename to openmc/plots.py
diff --git a/src/utils/openmc/settings.py b/openmc/settings.py
similarity index 100%
rename from src/utils/openmc/settings.py
rename to openmc/settings.py
diff --git a/src/utils/openmc/statepoint.py b/openmc/statepoint.py
similarity index 100%
rename from src/utils/openmc/statepoint.py
rename to openmc/statepoint.py
diff --git a/src/utils/openmc/summary.py b/openmc/summary.py
similarity index 100%
rename from src/utils/openmc/summary.py
rename to openmc/summary.py
diff --git a/src/utils/openmc/surface.py b/openmc/surface.py
similarity index 100%
rename from src/utils/openmc/surface.py
rename to openmc/surface.py
diff --git a/src/utils/openmc/tallies.py b/openmc/tallies.py
similarity index 100%
rename from src/utils/openmc/tallies.py
rename to openmc/tallies.py
diff --git a/src/utils/openmc/trigger.py b/openmc/trigger.py
similarity index 100%
rename from src/utils/openmc/trigger.py
rename to openmc/trigger.py
diff --git a/src/utils/openmc/universe.py b/openmc/universe.py
similarity index 100%
rename from src/utils/openmc/universe.py
rename to openmc/universe.py
diff --git a/src/utils/convert_binary.py b/scripts/convert_binary.py
similarity index 100%
rename from src/utils/convert_binary.py
rename to scripts/convert_binary.py
diff --git a/src/utils/convert_xsdata.py b/scripts/convert_xsdata.py
similarity index 100%
rename from src/utils/convert_xsdata.py
rename to scripts/convert_xsdata.py
diff --git a/src/utils/convert_xsdir.py b/scripts/convert_xsdir.py
similarity index 100%
rename from src/utils/convert_xsdir.py
rename to scripts/convert_xsdir.py
diff --git a/src/utils/memory_usage.py b/scripts/memory_usage.py
similarity index 100%
rename from src/utils/memory_usage.py
rename to scripts/memory_usage.py
diff --git a/src/utils/plot_mesh_tally.py b/scripts/plot_mesh_tally.py
similarity index 100%
rename from src/utils/plot_mesh_tally.py
rename to scripts/plot_mesh_tally.py
diff --git a/src/utils/statepoint_3d.py b/scripts/statepoint_3d.py
similarity index 100%
rename from src/utils/statepoint_3d.py
rename to scripts/statepoint_3d.py
diff --git a/src/utils/statepoint_histogram.py b/scripts/statepoint_histogram.py
similarity index 100%
rename from src/utils/statepoint_histogram.py
rename to scripts/statepoint_histogram.py
diff --git a/src/utils/tally_conv.py b/scripts/tally_conv.py
similarity index 100%
rename from src/utils/tally_conv.py
rename to scripts/tally_conv.py
diff --git a/src/utils/track.py b/scripts/track.py
similarity index 100%
rename from src/utils/track.py
rename to scripts/track.py
diff --git a/src/utils/update_inputs.py b/scripts/update_inputs.py
similarity index 100%
rename from src/utils/update_inputs.py
rename to scripts/update_inputs.py
diff --git a/src/utils/voxel.py b/scripts/voxel.py
similarity index 100%
rename from src/utils/voxel.py
rename to scripts/voxel.py
diff --git a/src/utils/xml_validate.py b/scripts/xml_validate.py
similarity index 100%
rename from src/utils/xml_validate.py
rename to scripts/xml_validate.py
diff --git a/src/utils/setup.py b/setup.py
similarity index 69%
rename from src/utils/setup.py
rename to setup.py
index 72682aea9..86047cc55 100644
--- a/src/utils/setup.py
+++ b/setup.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+import os
 from distutils.core import setup
 
 setup(name='openmc',
@@ -8,4 +9,5 @@ setup(name='openmc',
       author='Will Boyd',
       author_email='wbinventor@gmail.com',
       url='https://github.com/mit-crpg/openmc',
-      packages=['openmc'])
+      packages=['openmc'],
+      scripts=[os.path.join('scripts', f) for f in os.listdir('scripts')])