Current aqueous methods for removal of polymeric materials from the sidewalls of trenches etched into silicon wafers by reactive-ion-etching are inadequate for treating deep trenches having high aspect ratios. Spin-dry operations performed after the aqueous etching are incapable of completely removing rinse water and ionic species from these deep trenches, thereby leaving pockets of liquid. Subsequent evaporation of these pockets results in the concentration and eventual precipitation of residual ionic species creating watermarks. A two stage cleaning method is described in which the first stage dissolves the sidewall polymer and the second stage draws ionic species strongly chemisorbed onto the silicon surfaces into solution. A key feature of the method is that the wafer surface is not permitted to dry until after the final rinse.