From your description, I don't see why you need to do this in Perl. What's wrong with just renaming the folders?

On the other hand, if your source code references those directories and you need to do a global search-and-replace, you can do that with a one-liner:

perl -pi -0777 -e 's/c:\\base\\folder1/c:\\base\folder3\folder4/gis' *
[download]

You should probably back things up before you do this (you can also have perl create backups using the -i flag above, but then you have to go delete all those .bak files). Also, that will just change all the files in one directory. In unix, you could combine this with the find command to do it recursively. I'm not sure of the easiest way to do this in Windows.