KY(WO4)2 is a promising material for on-chip laser sources. Deep etching of small KY(WO4)2 samples in combination with various thin film deposition techniques is desirable for the manufacturing of such devices. There are, however, several difficulties that need to be overcome before deep etching of KY(WO4)2 can be realized in small samples in a reproducible manner. In this paper, we address the problems of (i) edge bead formation when using thick resist on small samples, (ii) sample damage during lithography mask touchdown, (iii) resist reticulation during prolonged argon-based inductively coupled plasma reactive ion etching (ICP-RIE), and (iv) redeposited material on the feature sidewalls. We demonstrate the etching of 6.5 µm deep features and the removal of redeposited material using a wet etch procedure. This process will enable the realization of waveguides both in ion-irradiated KY(WO4)2 as well as thin KY(WO4)2 membranes transferred onto glass substrate by bonding and subsequent polishing.