Sometimes there is a breakdown in terms between disciplines. Skinning, for the 3D artist, is a method of applying a rig to a model for animation purposes. Skinning, using the old real-time 3D game terminology, means to make a texture for the 3D model.

I am assuming the OP was about making a texture for the model. If so, then the model will need to be UV mapped (if it is not already) and then a texture created for it. There is no simple program for this. After all, how will the program know what kind of skin/texture you want to apply to your model? But there are various tools for UV mapping a model and for creating a texture.