In principle, you can use any substrate, since silicon doesn't really charge during e-beam exposure if properly grounded, unless you have wafers covered by an appropriate oxide layer. I would therefore not worry about the substrate in the first instance. Much more important are the parameters for the e-beam exposure, which need to be optimized in this respect, as well as the pattern design, the write mode and the choice of resist. There is also the question of the application, which may already favor a certain substrate material.