SEMs don't use light to create the image, instead a beam of electrons is fired at the surface and the ones which bounce back or are reemitted are detected. This gives a (very cool) looking picture that would be impossible to get with light but means that colours aren't detected...
The distinctive look of SEM images is because of the way edges of objects in the image appear; unlike most visible light photos the edges of objects are lighter than the middle. By detecting which way the slopes in the image are facing we can fake different coloured light falling onto the sample, I use a red light from the top, a green light from the bottom left and a blue light from the bottom right. This makes the image really come alive and gives it an even stronger sense of 3D.
Technically this colourisation method is mapping hues to the angle of orientation edges in the micrograph. The saturation of the illumination is based on the roughness of the texture at that point in the image and the value (brightness) is simply copied from the original micrograph.
The ImageJ macro I wrote to do this can be downloaded here.
Software used:
ImageJ
Image credit:
http://commons.wikimedia.org/wiki/File:Coleus_leaf_trichomes_SEM.jpg (public domain)