In this study, a self-assembled monolayer (SAM) of methoxy-poly (ethylene-glycol)-silane (mPEG-sil) was used to modify the silicon dioxide surface of polysilicon nanodevices (PNDs) to act as a passivation layer that inhibits nonspecific binding of proteins and reduces localized Joule heating power. Selective modifications of 3-aminopropyltrimethoxysilane (APTMS), NHS-biotin and dye-labeled Streptavidin on the removal regions were characterized. These PNDs, which consist of a two-level doping profile, were designed to confine heat in the low-level doping region during localized Joule heating. Localized Joule heating with pulse bias was examined in both vacuum and ambient, which indicated the removal region was longer in vacuum for the same pulse bias. Moreover, a comparison of selectively and nonselectively modified PNDs observed in time-lapsed fluorescence detection of dye-labeled Streptavidin showed a higher increasing rate in fluorescence intensity (∼2× enhancement) in the selectively modified PNDs. Finally, a COMSOL simulation was employed to evaluate the temperature distribution in the PNDs, with results showing that heat confinement was observed in the low-level doping region and a temperature very close to 673 K was achieved while applying a pulse voltage (40 V, 5 μs) to remove mPEG-sil.