Diatom-based silica nanostructures have drawn attention as high-value nanomaterials. However, removing organic matter from the diatom biomass is a critical step towards biogenic silica recovery. In the present study, chemical treatment: HCl, HNO₃, H₂O₂; high-temperature baking at 550 °C: 60 min, 120 min, 180 min; and oxygen plasma ashing: 30 min, 60 min, 90 min were employed for Denticula sp. cleaning to assess their relative efficiency and provide a quantitative assessment. Baking for 180 min gave the maximum organic matter removal (94.9 ± 0.8%) followed by plasma: 90 min (86.8 ± 1.2%) and HNO₃ (84.6 ± 1.3%) exposure. The CHN and FTIR results were in agreement with the trend observed in organics removal. However, in the case of baking and chemical exposure, the structure got damaged with disturbance in pore geometry, as revealed by FESEM and BET analysis. On the contrary, the plasma treatment resulted in un-damaged, negatively charged (−31.6 ± 1.4 mV), high surface area (81.6 ± 2.8 m² g⁻¹), mesoporous (24.6 ± 1.1 nm) structures, which makes it a right technique to process diatoms. Overall, plasma technology was found to be the most suitable method to recover high quality silica structures.