The use of e-beam based plasma as a source for plasma-polymer interactions was investigated employing two advanced photoresists that differed significantly in polymer structure. The influence of Ar+ bombardment energy, chemically-assisted etching using fluorine, and the effects of the presence of a thin fluorocarbon (FC) layer on surface roughness evolution and etching rates of the blanket photoresists were determined. Low energy ion bombardment increased surface roughness. Small amounts of fluorine (5% SF6/Ar), resulted in a further increase of the surface roughness and etch rate over values of Ar+ ion bombardment alone. An unexpected result was that the photoresist surface roughness evolved during the afterglow of an Ar plasma and decreased for long afterglows (300 ms). It was shown that the roughness of an FC overlayer impact the photoresist underlayer etching and surface roughening. The magnitude of the change was dependent on the conditions under which the FC overlayer is deposited.