Copper-free “click” chemistry on appropriately modified surfaces and photolithography were explored for site-directed immobilization of biomolecules. The surfaces were modified either with self-assembled monolayers of silanes or an epoxy resin and then used as they were or further modified through adsorption of rabbit gamma-globulins to increase their reactive amine-content. All surfaces were then reacted with a succinimidyl ester cyclooctyne derivative and the efficiency of each modification approach was determined through click reaction with an azide derivative of fluorescein. It was found that the highest fluorescence signal was provided by the surface that had been modified with the epoxy resin and then coated with rabbit gamma-globulins. Surfaces prepared following the different modification procedures have been analyzed with ToF-SIMS to gain insight into the chemical changes of the surfaces after each step of the modification procedure. Analysis of intensities of characteristic ions signals confirmed the successful outcome of click reaction following the proposed surface modification approach. In addition, the ability to define through photolithography areas for site-directed immobilization of biomolecules onto surfaces modified with the succinimidyl ester cyclooctyne derivative was demonstrated through the creation of two molecules patterns.