Two techniques, focused ion beam patterning, (FIB), and electron-beam lithography, (E-beam), for micron and submicron patterning of cross-linked poly(N- isopropylacrylamide) films are presented. Both techniques generate well-defined patterns that retain their thermo-responsiveness. However, only FIB patterning combined with soft lithography offers independent control over cross-link density and feature-size resolution. In order to demonstrate the use of E-beam lithography a series of "smart" trenches were fabricated, which could be exploited for BioSamples capture and release mechanisms for BioMEMS/NEMS sample processing.