The multichannel quartz crystal microbalance (MQCM) is very attractive for biosensor applications. The principle of the MQCM design involves fabricating arrays of quartz microbalances on a single substrate, and it is important that the individual sensor performance is not influenced by the neighboring devices. Feasible ways to control the coupling of acoustical energy within a MQCM structure are to increase the difference in the resonance frequency between the electroded and unelectroded portions of the substrate; and a practical way to achieve this is to use mesa structures. In this paper, the frequency interference between two mesa-shaped quartz crystal microbalances is investigated using Mindlin's theory. The results show that even a very small mesa height (approximately 5% of the plate thickness) can greatly reduce the frequency interference and more effectively trap the acoustic energy. This allows for a broader design window and higher packing density for MQCM applications.