Depends what your goal is.
If you want rename your autoexec.bat and config.sys to a backup name. Then during the Win95 install, have Windows load into a different directory. Windows will detect the previous install directory and suggest that the new one will be windows.000.
I would probably delete or rename the system files in the root of C also, like command.com, io.sys, msdos.sys (am I forgetting one??) That way you will not risk getting into a version conflict due to the Win95 Y2K patch and possibly other patches. You can do this with a windows boot disk in DOS mode, but you will need to use the attrib command to unhide those system files.
Conventional wisdom says to do a format and reinstall, but that is not always possible to preserve your data, unless you can back up to another drive.
BTW, which version of 95 are you working with?
viz