We discuss challenges involved in modelling different components of molecular devices and give several examples that demonstrate how computer modelling evolved over the last few years to become a comprehensive tool for designing molecules, predicting their adsorption and diffusion at surfaces, simulating atomic force microscopy imaging and manipulation of atoms and molecules at insulating surfaces and studying electron conduction in prototype molecular devices. We describe some of the computational techniques used for modelling adsorption, diffusion, imaging and manipulation of organic molecules at surfaces and challenges pertaining to these studies, give several examples of applications and discuss further prospects for theoretical modelling of complex organic molecules at surfaces.