First thing check if you have in fact gained any free space.
I suspect that you used the normal windows delete to delete the files and the long time was windows moving them to the recycle bin and renaming them. As one of our tests we deleted 55,000 small files to give us a benchmark if clients asked. The delete took just under the hour which we considered acceptable, we also regained all the space on the RAID 1 array.
As mdg has found using DOS delete is much faster because it only marks the files as deleted - it marks the space as being available. I suspect the DOS RD might be faster but we have not tested that.