I've only played with Autopsy and found it very lacking, so I stick with costly commercial Windows tools for forensic work. Having said that, I can't be positive, but Autopsy probably doesn't have the capacity to do what you want.
The reason has more to do with a the way forensic work is done, and with evidentiary procedure for courts. Normally, the way you work a forensics case, you work a forensically-correct image of the original disk. That image would be on a second disk, one that has specifically set up for forensics use. You recover the information there, and then transfer any files of interest to a third disk for presentation. This way the original disk is never harmed, as all work is done on the image on the second disk, and anything that gets touched by people after the fact is on third disk.
Really, what you want is a file-recovery tool, which is a very different function than forensic work. There are a number of other file recovery tools that will do what you want, and automatically move recovered files to a different disk/folder. A search for file recovery tools to find the feature you require, would probably be the best. One I use for Windows is Piriform's Recuva. http://www.piriform.com/recuva