This paper presents a systematic approach to fabricate optically smooth, through-wafer silicon (Si) molds for polymer optical devices, in particular poly(dimethylsiloxane) (PDMS) total internal reflection (TIR)-based devices. First, the Si molds were fabricated by an optimized, through-wafer deep reactive ion etching (DRIE) process to achieve small roughness. To further reduce the roughness, the Si molds were then oxidized and etched in BHF for three times to achieve surface roughness average (R a ) and root mean square (RMS) roughness below 25 nm while peakto-valley (P-V) roughness is below 150 nm. We monitored the surface roughness and morphology of the sidewalls of Si mold through three cycles of oxidation and BHF etching using field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM). We found that further oxidation and BHF etching might not have much effect in further reducing the roughness while the device feature definitions might be compromised. Finally, the PDMS TIR-based devices replicated from the Si molds were evaluated by means of FESEM, AFM and by imaging of the fluorescent evanescent spots.