Nowadays, 3D microoptical elements find a variety of applications from light emitting diodes and household appliances to precise medical endoscopes. Such elements, fabricated in a fused silica substrate by combining 3D e-beam patterning and dry etching, can be used as a mold for the high throughput replication in polymeric materials by UV nanoimprint technique. Flexible and precise control of 3D shape in the resist layer can be achieved by e-beam patterning, but it is also very important to know peculiarities of 3D pattern transfer from resist layer into the fused silica substrate. This paper reports on the effects of PMMA 3D microlens pattern transfer into fused silica substrate by CF4/O2 dry etching. It is demonstrated that etching rate ratio between PMMA and fused silica changes during plasma treatment. Thus, the resulting shape of transferred 3D profile is different from the shape in PMMA and this variation must be assessed during the design phase.