Using an inductively coupled plasma system, we study the effects of direct plasma, plasma-generated high-energy photons in the ultraviolet and vacuum ultraviolet (UV/VUV), and radical treatments on lipopolysaccharide (LPS). LPS is a biomolecule found in the outer membrane of Gram-negative bacteria and a potent stimulator of the immune system composed of polysaccharide and lipid A, which contains six aliphatic chains. LPS film thickness spun on silicon was monitored by ellipsometry while the surface chemistry was characterized before and after treatments by x-ray photoelectron spectroscopy (XPS). Additionally, biological activity was measured using an enzyme-linked immunosorbent assay under (a) a sensitive regime (sub-μM concentrations of LPS) and (b) a bulk regime (above μM concentrations of LPS) after plasma treatments. Direct plasma treatment causes rapid etching and deactivation of LPS in both Ar and H2 feed gases. To examine the effect of UV/VUV photons, a long-pass filter with a cut-off wavelength of 112 nm was placed over the sample. H 2 UV/VUV treatment causes material removal and deactivation due to atomic and molecular UV/VUV emission while Ar UV/VUV treatment shows minimal effects as Ar plasma does not emit UV/VUV photons in the transmitted wavelength range explored. Interestingly, radical treatments remove negligible material but cause deactivation. Based on the amphiphilic structure of LPS, we expect a lipid A rich surface layer to form at the air-water interface during sample preparation with polysaccharide layers underneath. XPS shows that H2 plasma treatment under direct and UV/VUV conditions causes oxygen depletion through removal of C-O and O-C = O bonds in the films, which does not occur in Ar treatments. Damage to these groups can remove aliphatic chains that contribute to the pyrogenicity of LPS. Radical treatments from both Ar and H2 plasmas remove aliphatic carbon from the near-surface, demonstrating the important role of neutral species.