Digital photocorrosion (DIP) of GaAs/AlGaAs nanoheterostructures has been found sensitive to semiconductor surface states and, thus, attractive for rapid detection of negatively charged bacteria in aqueous environment. However, calibration of DIP biosensors depends on the reproducibility of chipto-chip surface properties that are related to the chip fabrication process. To reduce the error related to this characteristics and provide a reference signal, we have examined the fabrication of biochips with a selective area removed biofunctionalization layer. The GaAs/AlGaAs biochips were coated with 1mM 16-mercaptohexadecanoic acid (MHDA) self-assembled monolayers (SAM) designed for interfacing antibodies suitable for immobilization of bacteria. Selective area thermal desorption of SAM was investigated with an Nd:YAG laser emitting at 1064 nm in a continuous wave mode. The exposure of a biofunctionalized and laser-processed chips to bacterial solution resulted in a selected area capture of bacteria. With a low-cost light emitting diode, this approach should allow the realization of an advanced DIP biosensor with a small surface area designed for referencing the photocorrosion process of a biosensor.