Context: Literature has no consensus over the utility of enameloplasty before fissure sealant placement. Aim: The objective of the study was to explore the effect of enameloplasty using a scanned electron microscope on the adaptability of resin-modified glass ionomer versus flowable resin-based sealants. Settings and Design: An in vitro, experimental study was done from July to November 2017 at the NED University and Dow University of Health Sciences, Karachi, Pakistan. Materials and Methods: An in vitro experimental study was done, for which twenty extracted human molars and premolars were selected. They were divided into two groups on the basis of sealant type (resin-modified glass ionomer versus flowable resin-based sealant). The groups were further subdivided on the basis whether these were subjected to enameloplasty or not. All specimens were thermocycled, sectioned, dried, and gold sputtered before inspection under a scanning electron microscope (×50). Statistical Analysis Used: The adaptability of the sealant material in the tooth fissures was assessed on an ordinal scale. SPSS version 23.0 was used for data analysis. Mann–Whitney U-test and ordinal regression were applied at 0.05 level of significance. Results: There were no statistically significant differences between adaptability scores achieved with resin-modified glass ionomer-based sealant and flowable resin-based sealant (P = 0.96). Moreover, enameloplasty resulted in inferior adaptability of the two sealant materials (P = 0.02). Conclusions: Enameloplasty has shown to exert a negative influence over adaptation of the sealant material into the tooth fissure irrespective of the sealant chemistry.