The nanoscale organization of acetylcholinesterase (AChE) and of its polyclonal antibody immobilized on gold thin films was studied by means of Energy Dispersive X-ray Reflectometry (EDXR) and Atomic Force Microscopy (AFM). The macromolecules were alternatively deposited over a self-assembled monolayer (SAM) of N-hydroxysuccinimide esters of thioctic acid. The measurements, collected in situ at subsequent deposition stages of the device, gave information on the distribution of the macromolecules on the surface showing that both the proteins can bind covalently to the SAM. In addition to this, we demonstrated that the antigen-antibody reaction takes place when one of the two reactants is anchored to the surface.