In this paper we present a simulation study that intends to characterize the influence of defects introduced by manufacturing processes on the geometry of a semiconductor structure suitable to be used as a multimode interference (MMI) 3 dB power splitter. Consequently, these defects will represent refractive index fluctuations which, on their turn, will drastically affect the propagation conditions within the structure. Our simulations were conducted on a software platform that implements both Beam Propagation and FDTD numerical methods. This work supports the development of a biomedical plasmonic sensor, which is based on the coupling between the propagating modes in a dielectric waveguide and the surface plasmon mode that is generated on an overlaid metallic thin film, and where the output readout is achieved through an a-Si:H photodiode. By using a multimode interference 1×2 power splitter, this sensor device can utilize the non-sensing arm as a reference one, greatly facilitating its calibration and enhanced performance. Amorphous silicon can be deposited by PECVD processes at temperatures lower than 300°C, an attractive characteristic which makes it back-end compatible to CMOS fabrication processes. As the spectral sensitivity of amorphous silicon is restricted to the visible range, this sensing device should be operating on a wavelength not higher than 700 nm, thus a-SiNx has been the material hereby proposed for both waveguides and MMI power splitter.