It sounds to me like you are asking about plugin architecture and sandboxing. Does that sound right?
The plugin component has been done and written about else where. SO has code examples on basic ways to import all the files.
The sandbox part is going to be a harder. Have a look at RestrictedPython and the Restricted Execution docs and the generally older but nevertheless helpful discussion of sandboxing.
If you aren't worried about untrusted code but rather want to isolate errors you could just wrap each module in a generic try/except that handles all errors. This would make debugging hard but would ensure that an error in one module didn't bring down the whole system.
If you aren't worried about untrused code but do need to have each file totally isolated then you might be best off looking into various systems of interprocess communication. I've actually had some luck using Redis for this (which sounds ridiculous but actually has been very easy and effective).
Anyway hopefully some of that helps you. Without more information it's hard to provide more than general thoughts and a guide to better googling.