Protein immobilization on surfaces is a critical step in the fabrication of protein based biosensors and biochips. This presentation investigates protein immobilization via covalent linkage on aldehyde-terminated self-assembled monolayers (SAMs). High resolution Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) are first used to examine the structure of methyl- and aldehyde-terminated alkanethiol SAMs/Au(111). In addition to the well known (root3xroot3)R30° basic periodicity and c(4x2) superstructures, our systematic STM investigations revealed a series of c(4x2) contrasts, which are due to the local density of states (LDOS) of the molecules, and not to the physical structure of the SAM. The molecular level structure of aldehyde-terminated SAMs is revealed for the first time by high resolution STM. The subsequent protein immobilization on fabricated aldehyde nanostructures is investigated in-situ by AFM. The protein attachment is found to depend sensitively on the local domain structure of aldehyde termini.