If you create a custom action with .Net, then a compatible version of .Net
must be installed.  However you could deploy your msi as part of a bundle,
and use the bootstrapper to install .net first as part of your chain, rather
than expecting the user to install .Net as a separate step.  You cannot
"remove" a dependency on .Net from a managed assembly. 
http://wixtoolset.org/documentation/manual/v3/bundle/

Certain versions of the OS ship with certain versions of .Net, so depending
on which OS you target you could make certain assumptions as to whether the
version of .Net you used is installed by default.   I think a best practice
would be to provide a bootstrapper or gracefully test for the version of
.Net that you require, in the event someone removes the .Net that you
expect.  Wix provides tools to add NetFx4x to a bundle's chain.

Alternatively, and my preference, create the custom action using native C++. 
The wix source has good examples of doing this and the wix libraries
(wcautil and dutil) really simplify C++ development.




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