It is often suggested that the growth in focused electron beam induced processing (FEBIP) is caused not only by primary electrons, but also (and even predominantly) by secondary electrons (SEs). If that is true, the growth rate for FEBIP can be changed by modifying the SE yield. Results from our Monte Carlo simulations show that the SE yield changes strongly with substrate thickness for thicknesses below the SE escape depth. However, our experimental results show that the growth rate is independent of the substrate thickness. Deposits with an average size of about 3 nm were written on 1 and 9 nm thick carbon substrates. The apparent contradiction between simulation and experiment is explained by simulating the SE emission from a carbon substrate with platinum deposits on the surface. It appears that the SE emission is dominated by the deposits rather than the carbon substrate, even for deposits as small as 0.32 nm3.