This work presents the surface modification of silicon chips as a platform for silicon-based biosensors with applications aiming for the detection of foodborne bacteria in aqueous solution. The detection requires high selectivity as the solution may contain a variety of biological species, which affect the outcome of the sensing process. The silicon surface is functionalized by a self-assembled monolayer (SAM) with thiol groups followed by immobilizing a thiol-linked DNA aptamer. The DNA aptamer used in this work has reported to recognize a biological species, E. coli ATCC 25922. The presence of DNA aptamer on the sensor surface allows the capture of the specific E. coli cells on the surface, while other potential biological (and chemical) species would not attach to the sensor surface, thus improving the selectivity of the sensor. The uniform formation of the SAM on the surface is an important step toward uniformly coating the sensor surface with the desired DNA aptamer. The SAM is created on the silicon surface by surface modification with the MPTS (3-mercaptopropyl trimethoxy silane) solution. Then the aptamer DNA solution is applied as droplets on the chip followed by a cure process. The attachment of the SAM and DNA aptamers are verified by atomic force microscopy (AFM). The surface functionalization presented in this work can be used for sensors made of silicon coated with a thin layer of native oxide, and can be adopted for detection of other cells and biological agents using the proper SAM and DNA aptamer.