Soft lithography offers great potential for the fabrication of 2D and 3D patterned structures using a variety of materials and patterns. It complements and extends conventional fabrication methods. This thesis is particularly focus on microcontact printing (μCP) as a method to create biological patterns on surfaces and also as a tool used in “in-situ” synthesis. Microcontact printing has unique features that make this technique very attractive: (i) it is simple to introduce in any laboratory, (ii) it is biocompatible, (iii) it can fabricate features below 100 nm, (iv) it is applicable to broad range of materials, (v) it is efficient and not expensive. The important feature is that stamp which is used for printing is flexible and can seal conformally to the surface tolerating the nanoscale roughness. In this thesis the focus is on the application of soft lithography in the fabrication of microsystems useful in studying interactions between biomolecules and cells.