Controlling the sensing properties of a silicon nanowire field effect transistor is dependent on the surface chemistry of the silicon nanowire. A standard silicon nanowire has a passive oxide layer (native oxide), which has trap states that cause sensing inaccuracies and desensitize the surface to nonpolar molecules. In this paper, we successfully modified the silicon nanowire surface with different nonoxide C3 alkyl groups, specifically, propyl (Si-CH2-CH2-CH3), propenyl (Si-CH═CH-CH3), and propynyl (Si-C≡C-CH3) modifications. The effect of the near surface bond on the sensor sensitivity and stability was explored by comparing three C3 surface modifications. A reduction of trap-states led to greater sensor stability and accuracy. The propenyl-modified sensor was consistently the most stable and sensitive sensor, among the applied sensors. The propenyl- and propynyl-modified sensors consistently performed with the best accuracy in identifying specific analytes with similar polarity or similar molecular weights. A combination of features from different sensing surfaces led to the best rubric for specific analytes identification. These results indicate that nonoxide sensor surfaces are useful in identifying specific analytes and that a combination of sensors with different surfaces in a cross-reactive array can lead to specific analytes detection.