I've never used a makerbot scanner, so perhaps take what I'm saying with a pinch of salt, but I'd be surprised if you would want to cover it in scribbles. It is presumably referencing itself through the turntable, and all it is doing is measuring laser time to the surface of the object, so the more consistent the surface the better.

A developer spray is probably best but again a light (not black) matte paint will be fine. If you don't want to paint it then put some car polish on it and let it dry. It will dull the surface.

A high contrast background is no problem, but be careful it's not causing additional noise (e.g. if it was shiny.)

Have you got a picture of the mouse you're looking to scan? Will be easier to recommend what programs to use.

The free programs are a long way away from the commercial ones. For merging and clean up I'd probably start by downloading a trial of Geomagic Studio. Lot of options if you want to solid/surface model it...