You don't state which model scanner you're talking about, but in ProScan you can go to the Test & Extras tab, type MSM,1 in the Protocol Command box, then hit Send.
EDit: Hmm, I suppose the scanner would already need to be in Serial Mode for that to work.
In the future, if you're wanting to get the scanner into Mass Storage Mode from ProScan, use that MSM command but set the timer (in seconds) to something reasonable. After the timer expires, the scanner will reboot and go back to Serial Mode.
MSM,120 for example would reboot to Serial Mode after 2 minutes.