Forensic analysis of DNA from non-human bones can be important in investigating a variety of forensic cases. However, decomposed bone is difficult to process for isolating DNA. In this study, a previously established enzymatic method was utilized to process bone samples that simulate decomposed specimens. Our results demonstrated that this enzymatic processing method is effective for removing decomposed soft tissues and outer surface materials such as mineralized bone connective tissue of bone fragment samples. Our data suggested that this method can be used in the initial sample preparation for cleaning the outer surface of decomposed non-human skeletal fragments. This study introduced an alternative method for processing decomposed non-human bone evidence prior to DNA isolation. Such a method can potentially be used to process various samples of different sizes and conditions for the investigation of a wide variety of criminal cases involving animals.