We present the study of the effects of high energy cosmic rays (CRs) over the astrophysical ices, observed toward the embedded class I protostar Elias 29, by using computational modeling and laboratory data. Its spectrum was observed with {it Infrared Space Observatory - ISO}, covering 2.3 - 190 $mu$m. The modeling employed the three-dimensional Monte Carlo radiative transfer code RADMC-3D (Dullemond et al. 2012) and laboratory data of bombarded ice grains by CRs analogs, and unprocessed ices (not bombarded). We are assuming that Elias 29 has a self-irradiated disk with inclination $i =$ 60$^{circ}$, surrounded by an envelope with bipolar cavity. The results show that absorption features toward Elias 29, are better reproduced by assuming a combination between unprocessed astrophysical ices at low temperature (H$_2$O, CO, CO$_2$) and bombarded ices (H$_2$O:CO$_2$) by high energy CRs. Evidences of the ice processing around Elias 29 can be observed by the good fitting around 5.5-8.0 $mu$m, by polar and apolar ice segregation in 15.15-15.25 $mu$m, and by presence of the CH$_4$ and HCOOH ices. Given that non-nitrogen compounds were employed in this work, we assume that absorption around 5.5-8.0 $mu$m should not be associated with NH$_4^+$ ion (Shutte & Khanna2003), but more probably with aliphatic ethers (e.g. R1-OCH$_2$-R2), CH$_3$CHO and related species. The results obtained in this paper are important, because they show that the environment around protostars is better modeled considering processed samples and, consequently, demonstrates the chemical evolution of the astrophysical ices.