diff --git a/docs/source/io_formats/index.rst b/docs/source/io_formats/index.rst
index bc5b0a4a91..7ae22c0a33 100644
--- a/docs/source/io_formats/index.rst
+++ b/docs/source/io_formats/index.rst
@@ -44,7 +44,6 @@ Output Files
 
    statepoint
    source
-   surface_source
    summary
    depletion_results
    particle_restart
diff --git a/docs/source/io_formats/statepoint.rst b/docs/source/io_formats/statepoint.rst
index 92b103ef7f..46725fa8b9 100644
--- a/docs/source/io_formats/statepoint.rst
+++ b/docs/source/io_formats/statepoint.rst
@@ -162,5 +162,5 @@ All values are given in seconds and are measured on the master process.
              source sites between processes for load balancing.
            - **accumulating tallies** (*double*) -- Time spent communicating
              tally results and evaluating their statistics.
-          - **writing statepoints** (*double*) -- Time spent writing statepoint
-            files
+           - **writing statepoints** (*double*) -- Time spent writing statepoint
+             files
diff --git a/docs/source/methods/cross_sections.rst b/docs/source/methods/cross_sections.rst
index c360805bea..dc42d33de5 100644
--- a/docs/source/methods/cross_sections.rst
+++ b/docs/source/methods/cross_sections.rst
@@ -186,10 +186,10 @@ The data governing the interaction of particles with various nuclei or materials
 are represented using a multi-group library format specific to the OpenMC code.
 The format is described in the :ref:`mgxs_lib_spec`. The data itself can be
 prepared via traditional paths or directly from a continuous-energy OpenMC
-calculation by use of the Python API as is shown in the
-:ref:`notebook_mg_mode_part_i` example notebook. This multi-group library
-consists of meta-data (such as the energy group structure) and multiple `xsdata`
-objects which contains the required microscopic or macroscopic multi-group data.
+calculation by use of the Python API as is shown in an `example notebook
+<../examples/mg-mode-part-i.ipynb>`_. This multi-group library consists of
+meta-data (such as the energy group structure) and multiple `xsdata` objects
+which contains the required microscopic or macroscopic multi-group data.
 
 At a minimum, the library must contain the absorption cross section
 (:math:`\sigma_{a,g}`) and a scattering matrix. If the problem is an eigenvalue
diff --git a/docs/source/usersguide/cross_sections.rst b/docs/source/usersguide/cross_sections.rst
index 74267c9c08..bc5b3436fd 100644
--- a/docs/source/usersguide/cross_sections.rst
+++ b/docs/source/usersguide/cross_sections.rst
@@ -124,7 +124,7 @@ OpenMC.
 .. hint:: The :class:`IncidentNeutron` class allows you to view/modify cross
           sections, secondary angle/energy distributions, probability tables,
           etc. For a more thorough overview of the capabilities of this class,
-          see the :ref:`notebook_nuclear_data` example notebook.
+          see the `example notebook <../examples/nuclear-data.ipynb>`__.
 
 Manually Creating a Library from ENDF files
 -------------------------------------------
@@ -252,8 +252,8 @@ However, if  obtained or generated their own library, the user
 should set the :envvar:`OPENMC_MG_CROSS_SECTIONS` environment variable
 to the absolute path of the file library expected to used most frequently.
 
-For an example of how to create a multi-group library, see
-:ref:`notebook_mg_mode_part_i`.
+For an example of how to create a multi-group library, see the `example notebook
+<../examples/mg-mode-part-i.ipynb>`__.
 
 .. _NJOY: http://www.njoy21.io/
 .. _NNDC: https://www.nndc.bnl.gov/endf
diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst
index bc7a2214b8..ab2fe2f120 100644
--- a/docs/source/usersguide/install.rst
+++ b/docs/source/usersguide/install.rst
@@ -12,11 +12,11 @@ Installation and Configuration
 Installing on Linux/Mac with conda-forge
 ----------------------------------------
 
-`Conda <http://conda.pydata.org/docs/>`_ is an open source package management
-system and environment management system for installing multiple versions of
-software packages and their dependencies and switching easily between them. If
-you have `conda` installed on your system, OpenMC can be installed via the
-`conda-forge` channel. First, add the `conda-forge` channel with:
+Conda_ is an open source package management system and environment management
+system for installing multiple versions of software packages and their
+dependencies and switching easily between them. If you have `conda` installed on
+your system, OpenMC can be installed via the `conda-forge` channel. First, add
+the `conda-forge` channel with:
 
 .. code-block:: sh
 
@@ -25,16 +25,16 @@ you have `conda` installed on your system, OpenMC can be installed via the
 To list the versions of OpenMC that are available on the `conda-forge` channel,
 in your terminal window or an Anaconda Prompt run:
 
-.. code-block:: sh 
+.. code-block:: sh
 
     conda search openmc
-    
+
 OpenMC can then be installed with:
 
 .. code-block:: sh
 
     conda create -n openmc-env openmc
-    
+
 This will install OpenMC in a conda environment called `openmc-env`. To activate
 the environment, run:
 
@@ -424,7 +424,7 @@ distributions.
 
    `pandas <http://pandas.pydata.org/>`_
       Pandas is used to generate tally DataFrames as demonstrated in
-      :ref:`examples_pandas` example notebook.
+      an `example notebook <../examples/pandas-dataframes.ipynb>`_.
 
    `h5py <http://www.h5py.org/>`_
       h5py provides Python bindings to the HDF5 library. Since OpenMC outputs
@@ -509,7 +509,6 @@ schemas.xml file in your own OpenMC source directory.
 .. _GNU Emacs: http://www.gnu.org/software/emacs/
 .. _validation: https://en.wikipedia.org/wiki/XML_validation
 .. _RELAX NG: http://relaxng.org/
-.. _NNDC: http://www.nndc.bnl.gov/endf/b7.1/acefiles.html
-.. _ctest: http://www.cmake.org/cmake/help/v2.8.12/ctest.html
-.. _Conda: https://docs.conda.io/en/latest/
+.. _ctest: https://cmake.org/cmake/help/latest/manual/ctest.1.html
+.. _Conda: https://conda.io/en/latest/
 .. _pip: https://pip.pypa.io/en/stable/
diff --git a/docs/source/usersguide/processing.rst b/docs/source/usersguide/processing.rst
index 210caca820..9652a51ca6 100644
--- a/docs/source/usersguide/processing.rst
+++ b/docs/source/usersguide/processing.rst
@@ -34,13 +34,13 @@ as requested; it is used in many of the provided plotting utilities, OpenMC's
 regression test suite, and can be used in user-created scripts to carry out
 manipulations of the data.
 
-An :ref:`example IPython notebook <notebook_post_processing>` demonstrates how
-to extract data from a statepoint using the Python API.
+An `example notebook <../examples/post-processing.ipynb>`_ demonstrates how to
+extract data from a statepoint using the Python API.
 
 Plotting in 2D
 --------------
 
-The :ref:`IPython notebook example <notebook_post_processing>` also demonstrates
+The `notebook example <../examples/post-processing.ipynb>`_ also demonstrates
 how to plot a structured mesh tally in two dimensions using the Python API. One
 can also use the :ref:`scripts_plot` script which provides an interactive GUI to
 explore and plot structured mesh tallies for any scores and filter bins.
@@ -101,5 +101,5 @@ For eigenvalue problems, OpenMC will store information on the fission source
 sites in the statepoint file by default. For each source site, the weight,
 position, sampled direction, and sampled energy are stored. To extract this data
 from a statepoint file, the ``openmc.statepoint`` module can be used. An
-:ref:`example IPython notebook <notebook_post_processing>` demontrates how to
+`example notebook <../examples/post-processing.ipynb>`_ demontrates how to
 analyze and plot source information.