This work is about the detailed investigation of the changes of the surface topography, the degree of compaction/shrinkage and its relation to the irradiation fluence and the structure spacing in poly(dimethylsiloxane) (PDMS) patterned with 2MeV proton microbeam. The irradiated periodic structures consisted of parallel lines with different widths and spacing. To achieve different degrees of compaction, each structure was irradiated with more different fluences. At the irradiated areas the surface topography, the adhesion, the wettability and the rigidity of the surface also changes due to the chemical/structural change of the basic poly(dimethylsiloxane) polymer. The surface topography, the phase modification of the surface, and the connection between them was revealed with using an atomic force microscope (AFM). (C) 2010 Elsevier B.V. All rights reserved.