If you cut the shaft yourself, an easy way to keep the motor clean is to partially inflate a balloon, press the motor shaft into the balloon and then the motor into the balloon, envelope the motor and then let the air out of the balloon while pressing further, thusly putting the motor inside the balloon. Then just poke the motor shaft out and have at it.
I assume you know how to get the motor out of the balloon afterwards.
By the way, this also works for fiberglassing parts. apply resin, fiberglass, more resin, squeagy off most of te resin, Balloon the part and then squegy out any wrinkles.