If I get you right... Let's suppose there's a folder structure:
my_folder\
subfolder1\
file1.txt
subfolder2\
file2.txt
subfolder3\
file3.txt
You can enter my_folder\, switch to "Flat" mode (via Ctrl+Shift+B or "View mode" button in the top right corner of the explorer panel). It will show all the files recursively within one list:
my_folder\
file1.txt
file2.txt
file3.txt
Now you can select these files and multi-rename them.