Objectives This study aims to assess the obturation efficacy of sealers placed with different techniques using microcomputed tomography (µCT) and assess the influence of µCT testing parameters on the obturation data obtained. Materials and methods Incisors and mesial roots of lower molars with standardized root length were scanned using µCT, and one tooth of each type was 3D printed in acrylic. Two obturation techniques (warm vertical and single cone) and 4 sealer types (AH Plus, BioRoot RCS, Totalfill BC, and Bio-C Sealers) were assessed following storage in Hank’s balanced salt solution for 3 and 6 months by assessing gap and void volume percentages on both natural and replica incisor and molar roots. The storage solution was analysed to assess calcium ion leaching. The influence of temperature, tooth positioning, and moisture content of the teeth while µCT scanning was also investigated. Results The obturation quality in the incisor group was the same using both natural teeth and replicas (p > 0.05). No changes in void volume were identified when comparing the same sealer using different obturation techniques. The premixed sealers used in single-cone obturation exhibited high void volume in the 3D printed replicas in the long term. The temperature, positioning, and moisture content of the teeth did not affect the outcome of µCT testing. Conclusions BioRoot RCS, Totalfill BC, and Bio-C Sealers are suitable for obturation of both complex and simple root canal systems using different obturation techniques with BioRoot RCS exhibiting the highest calcium ion release. 3D printed acrylic teeth can be used to assess the obturation quality in uncomplicated root canal systems. µCT parameters had no significant effect on the µCT measurement. Clinical relevance The single-cone obturation technique with hydraulic sealer is a simple technique that can be used for obturation of all root canal systems.