In the present paper we report on the modifications induced by low energy particle beams (1–5 keV He +, Ar +, N + 2, He 0, N 0 2 and H 0 2) on the chemical structure, optical properties and surface morphology of silicon-based polymer, poly-hydroxy-methyl-siloxane (PHMSO). The in situ XPS analysis shows that ion irradiation induces depletion of C atoms and progressive enrichment of Si and O atoms within the irradiated layers, yielding a ceramic-like SiO x C y H z phase of variable composition. For a given projectile, a steady state composition is reached in any case above the fluence of 1 × 10 16 particles/cm 2. The most efficient conversion to a ceramic-like layer, with a final composition SiO 1.85–1.89C 0.3–0.4 H z , is obtained by using 5 keV He + beams, while N + 2 and Ar + seem less effective. At variance of this, a dramatic carbon enrichment is observed when the PHMSO films are irradiated with fast neutral particles (FAB treatments). The optical measurements show that in general the beam-converted layers remain practically absorption-less, while the relevant features of the reflectivity spectra (positions of maxima and minima) critically depend upon the type of projectile. Thus, 5 keV He + ion irradiation induces the shift of the reflectivity maxima to shorter wavelengths (blue shift), while 5 keV N + 2 ions induce no shift and irradiation with N 2 or H 2 neutral beams induce a red shift. The AFM measurements show that also the surface morphology critically depends on the nature of the irradiating particles. Thus, 5 keV He + irradiation produces films as flat as the original polymer surface, while irradiation with Ar + (inducing a lower degree of conversion) increases the roughness, N + 2 irradiation induces characteristic undulations of the surfaces and FAB treatments induces a much higher surface roughening. The experiments show clearly that both the compositional modifications and the irradiation-induced nanometer scale morphological features critically determine the optical properties of the irradiated materials.