I found this post really useful for recursively locating and deleting Thumbs.db files in subfolders. This comes in handy especially when you're checking whether two folders are equal, based on size, but there are lots of Thumbs.db files running around that make life difficult.
In a nutshell, first go to the folder you're inspecting in cmd. Then, locate Thumbs.db files like this:
dir thumbs.db /a /b /s
...and delete them like this:
del thumbs.db /a /s
Read the whole article for full details (including PowerShell commands).