well, you could change the security on the root folder, in advanced, make it so your users have modify on "this folder only"
then, if all 50 subfolders get the same security as the other subfolders, you can select all the folders at the same time, right click properties, security - it will ask you if you want to make them all the same, say yes.... then adjust from there... advanced, uncheck inherit from parent, give them their modify permissions here and include subfolders
if they need different security from each other, then, you're going to have to do each subfolder individually... but you -might- be able to get someone in a scripting category here to write you a batch file that you can run in the root folder, which captures a (dir /b) listing, pumps it thru a loop that runs cacls.exe over each result, using if/then for directory names, but that's going to be harder than just doing it by mouse.