Microcantilever based sensors can be used for quantitative analysis of the nanomechanical response associated with conformational change and the corresponding charge transduction during molecular interaction. A specific aptamer is used for Malachite Green (MG) recognition, and two different immobilization methods are investigated, single thiolation and double thiolation. The surface stress changes due to the aptamer-ligand binding are measured with differential interferometry techniques and the sensitivity of the two different methods are compared. The findings show that the double thiolation method has a significant improvement on the threshold sensitivity of the sensing system.