The purpose of this in vitro study was to compare of a 1, 4 and 8 min. immersions in acidulated phosphated fluoride gel (1.23% APF gel, Sultan Topex), a Fluoride Varnish (Fluor Protector® 1% difluorsilane, 0.1% fluoride) and water on surface topography of two different fissure sealants (Helioseal®Clear, Helioseal®F). 28 samples were prepared into seven groups. The surface topography of two scanning electron micrographs of each specimen was scored visually by two investigators. Inter rater reliability was r = 0.74 (intraclass correlation coefficient) for scoring all micrographs. No significant difference in intra-investigator scores was found. No significant differences in the mean visual scores were found among the 1-min treatment groups (APF gel and Fluoride Varnish). Significantly higher mean visual scores were found for all the specimens immersed for 8- min in APF gel (p=0.000). Significantly higher mean visual scores were found for Helioseal®F immersed for 8-min in APF gel (p=0.02).