A novel MEMS-based modulation scheme is presented as a method to enhance the signal-to-noise ratio (SNR) of silicon photodiodes adapted for the detection of light-emitting bio-reporter signals. Photodiodes are an attractive photodetector choice because they are VLSI compatible, easily miniaturized, highly scalable, and inexpensive. Silicon photodiodes exhibit a wide response range extending from the ultraviolet (UV) to the near infrared (IR) part of the spectrum, which in principle is appropriate for sensing low intensity optical signals. Silicon photodiodes, however, exhibit limited sensitivity to optical dc signals, as the magnitude of the low frequency noise is comparable to signal magnitude. Optical modulation prior to photodetection overcomes the inherent low frequency noise of photodetectors and system detection circuits. The enhancement scheme is based on a design of high frequency optical modulators that operate in the 1-2 kHz range in order to overcome the low frequency spectral noise. We have denominated this MEMS-based scheme Integrated Heterodyne Optical System (IHOS). The modulation efficiency of the proposed architecture can reach up to 50 percent. In order to implement the MOEMS optical modulators, a new two-mask fabrication process was developed that combines high-aspect ratio and low aspect ratio structures at the same device layer (aspect ratio is defined as a ratio between the structure height to its width). Long stroke electrostatic combdrive actuators integrated with folded flexures (high aspect-ratio) were fabricated together to drive large aperture shutters (low aspect ratio). We have denominated this process MASIS (Multiple Aspect Ratio Structural Integration). Under resonant excitation at approximately 1 kHz, MOEMS modulators demonstrated maximum displacement of about 40 microns at an actuation voltage of 15 V peak in air, and 3.5 V peak in vacuum (8 mTorr). Results of analytical solutions and finite element analysis (FEA) simulations are in good agreement with experimental data. A comprehensive model was developed that demonstrates the effective use of IHOS as a SNR enhancer of photodiode sensitivity, providing a 30 dB improvement in the detection limit. This work represents the first attempt for signal enhancement utilizing MEMS technology for detection of low intensity optical signals, and particularly for low intensity optical bio-reporter signals of whole-cell sensors. Whole-cell sensors are genetically modified cells that can be engineered to act as chemical-optical transducers. As the cells are exposed to toxins, photo-emission (bioluminescence) is triggered, providing optical emission levels per cell proportional to the toxicity concentration in the environment. The most important application that we are currently investigating is the implementation of whole-cell sensors as an early detection method against bio-terrorism. Bioluminescence detection becomes a very challenging task, as the maximum photo-emission rate per cell is limited to 300 photons/sec. The main intended application of the IHOS is to utilize it as a seamless add-on that will be placed in between photodiodes and whole-cell sensors, all of which combined into an inexpensive and portable toxicity reader. We believe that the ramifications of this new MEMS-based scheme can be also applicable to a vast number of applications for optical systems in which the SNR needs to be improved.