I am currently trying to remove an old Motor Guide from my Ranger 364V and the mount will not come off.  I opened up the front panel and it turns out the screws are held down on the bottom with rubber washers.  How do I get the screws out?  I have tried cutting the washers, but that isn't working.

So there is no nut on the bottom? Just rubber washers? That doesnt sound right but if thats the case, get yourself a Dremel and a cutting disc and go to work.

Every trolling motor I've ever removed involved one guy up top on the screw/bolt turning it while someone, usually with skinny arms, holding the nut with a wrench.

  I'm pretty sure there is a nut inside the rubber and both are locked on.  One of the screws came off really easily in the beginning so I can try cutting that off and report back.  I wish they would all just unscrew like that first one

What you are describing sounds like isolators

http://www.motorguide.com/store/accessory/mounting/mounting-isolators

There is a nut at the bottom of these that allows the bolt to catch and the rubber is compressed to hold the mount on. Normally you just unscrew the bolts but they could be seized. Maybe try spraying with some sort of penetrant. You may have to cut them with a  dremel or some sort of power tool.

I had that trouble once before i drilled the head of the bolt off took a punch and pushed them down through

and the rubbers with the bolt worked there way back to the bilge area over time