It's not possible to search by OU with FileLocator Pro. However, if you have a list of folders you'd like to search you can save that to a text file and load it into FileLocator Pro.
For example, if you had a text file with something like:
You could load that into FileLocator Pro, e.g.
File name: *.pdf
Containing Text: Search Terms
Look In: =C:\Lists\NetworkComputers.txt
The '=' prefix instructs FileLocator Pro to load the Look In value from the file.