The current in vitro study’s objective was to evaluate the micromorphological changes in dentin after removal of caries with conventional rotary or enzyme-based CMCR agent. Fourteen cavitated carious freshly extracted human permanent molars were collected for the study. The root of each molar was sectioned and discarded, while the crowns were fixed to resin blocks. The specimens were randomly divided into two groups, with 7 specimens in each group (n =7), group (1): conventional rotary method, group (2): enzyme-based CMCR agent. Each tooth was evaluated for micromorphological analysis under scanning electron microscopy (SEM). The SEM observations revealed presence of smear layer after rotary caries removal and showed little or no smear layer after enzyme-based caries removal.This means that Enzyme papain-based CMCR agent is a reliable alternative to conventional rotary method.