Background: Sealers are necessary along with solid core material. The sealers exert their effect more effectively when they tend to penetrate the dentinal tubules. The latter is enhance by preparation with a rotary file system. In clinical practice numerous file system and sealers are available commercially. This study was an attempt to evaluate the effective of single and multiple rotary file system in preparing a tooth surface more conductive to sealer penetration. Different category of sealer were also evaluated for comparative penetration Objective: To compare the penetration of different sealers after biomechanical preparation with different file systems. Material and Method: 90 freshly extracted human permanent mandibular premolar were selected on the basis of predetermined inclusion and exclusion criteria, and equally divided into three groups.In Group 1 teeth were prepared with Hand K files using step back technique, In Group 2 teeth were prepared with HeroShaper using crown down technique, In Group 3 teeth were prepared with OneShape rotary file using crown down technique and samples were sectioned at coronal, middle, apical third. The prepared samples were analyzed for depth of penetration of sealer using confocal scanning microscope. The data obtained was subjected to statistical analysis using One-way ANOVA, Repeated measures ANOVA and LSD Post Hoc test. Result: Depth of penetration of different sealers was found to be significantly higher in samples prepared with OneShape than the HeroShaper and Hand K file. Depth of penetration in coronal third was found to be significantly higher than middle and apical third. Depth of penetration with AH Plus was found to be significantly higher than that of EndoREZ and RoekoSeal. Conclusion: AH Plus displays highest penetration amongst the tested sealers and preparing the canal with OneShape leads to higher sealer penetration.