Well it depends how many loose files are in the folder. For instance say I have 10,000 pictures in one folder and that folder when I open it is taken for ever to load cause it is trying to cache all the contents and index all those files that are contained in it. If I go into that particular folder and create more folders lets say 10 folders, then place 1000 pictures in each folder then it will load a lot faster cause there not so many files in one folder to cache and index. Try and keep you files down to a moderate number of files inside the folders. It's like trying to stuff a bunch of paper inside a manilla folder it can only hold so many before it doesn't function any more....
Also most USB drives go idle and stop spinning after about 15 minutes usually, you can use the software that came with the drive to configure the usb to spin all the time. A 3tb drive is huge and I would consider partitioning the drive to 3 separate partitions of 1tb each that would speed things up considerably. Also 2tb is all that windows will see on a MBR partition if you want to keep it at 3tb then you will have to set it at a GPT (GUI Partition Table) for it to be used correctly in Windows 7.
Follow this tutorial on how to change the partition table from mbr to gpt:
Convert MBR Disk to GPT Disk