Ga implantation into Si and reactive ion etching has been previously identified as candidate techniques for the generation of 3D nanopatterns. However, the structures manufactured using these techniques exhibited impedingly high surface roughness. In this work, we investigate the source of roughness and introduce a new patterning process to solve this issue. The novel patterning process introduces an additional layer absorbing the implanted Ga, thus preventing the clustering of the implanted Ga observed with uncoated Si substrates. This process enables 3D nanopatterning with sub-100 nm lateral resolution in conjunction with smooth height transitions and surface roughness down to 4 nm root mean square. Such patterns are ideally suited for optical applications and enable the manufacturing of nanoimprint lithography templates for low-profile Fresnel lenses.