# Note that this is also just a quick scribble and you may need to adapt this to your needs
# Folders
dir /b /s /a:d | perl -ne "print $_ if $_=~/^c:\\myinputpath\\.*?\\myfolder\\.*?$/" > filesconfig.txt
# Files
dir /b /s | perl -ne "print $_ if $_=~/^c:\\myinputpath\\.*?\\myfolder\\filenames.*?$/" > foldersconfig.txt