I have used Wings 3D (http://www.wings3d.com) for just that purpose. It is very easy to use, and has many other useful functions built in. Not only can you reform the mesh, but you also you have the ability to import and export many other meshes such as .obj, and etc. When you have completed your modifications you can export them in one of several formats (I find it easier to just keep it in .stl) and then use netfab (also has a free version with some limitations as compared to the paid version) to fine tune the mesh if it is not printable in its current format. Wings will export your modifications in .stl format, but you may have to fine tune to get rid of holes blemishes and etc., and you can view your changes in several views such as Gaussian and other forms.
If you decide to try Wings 3D you need to go through the tutorials, since there is a multitude of possibilities, including making your own meshes, beginning with several basic forms such as squares, cubes, cylinders and several other basic geometrical figures.
Using these two programs I have been able to modify many meshes and arrive at a very printable object. One of the features of Wings which has been quite valuable is the smoothing app which reduces the sharp division lines on some models.
Since both programs are free you can try them and uninstall them if they do not fill your needs. Blender is also an excellent free program, but I find Wings to be much simpler to use.
Hope this helps