In this paper, we describe a self-aligned fabrication method for a nano-patterned bottom electrode using flood exposure from the backside. Misalignments between layers could cause the final devices to fail after the fabrication of the nano-scale bottom electrodes. A self-alignment was exploited to embed the bottom electrode inside the glass substrate. Aluminum patterns act as a dry etching mask to fabricate glass trenches as well as a self-aligned photomask during the flood exposure from the backside. The patterned photoresist (PR) has a negative sidewall slope using the flood exposure. The sidewall slopes of the glass trench and the patterned PR were $54.00^{circ}$ and $63.47^{circ}$, respectively. The negative sidewall enables an embedment of a gold layer inside $0.7{mu}m$ wide glass trenches. Gold residues on the trench edges were removed by the additional flood exposure with wet etching. The sidewall slopes of the patterned PR are related to the slopes of the glass trenches. Nano-scale bottom electrodes inside the glass trenches will be used in beam resonators operating at high resonant frequencies.