Proton beam writing is a maskless lithographic technique for the fabrication of 3D micro and nano structures in polymers. The fabricated structures find application in micro fluidics, optics, biosensors, etc. We use proton beam writing for micro-patterning in polymers which will facilitate fabrication of test structures for micro-components of micro-fluidic devices, organic thin film transistors (OTFT) and organic light emitting diodes (OLED). In this paper we report fabrication of varying width micro channels in PMMA and SU-8 films used as positive and negative resists respectively. The patterns were written using 2 MeV proton beam focused down to around 1 micron. We have achieved clean periodic micro-channels of width varying from few micrometers to wider ones in both the resists. Being a mask less lithography it provides an efficient way of reducing turnaround time for test structures with several channel widths and patterns being conveniently written at the same development cycle. Possible applications of the patterned structures in OLED/TFT are discussed. Additional structures like checkered board are also fabricated. Optimized fluence for both the resist has been determined. (C) 2011 Elsevier B. V. All rights reserved.