This study is aimed at comparing the efficacy of heat softening and ultrasonic removal of root-end gutta-percha during retrograde preparation for root apical microsurgery. Recently extracted single-rooted premolars (
n
=
40
) were prepared with standardized endodontically treated and root-end resection and then randomly divided into four groups that received root-end cavity preparation using four different instruments: a diamond-coated ultrasonic tip (AS3D; SACTEON, Paris, France), AS3D with the modified plugger of cordless heat carrier (MSE; B&L Biotech, Bala Cynwyd, PA, USA), stainless steel ultrasonic tip (Jetip-2; B&L Biotech, Bala Cynwyd, PA, USA), or Jetip-2 with MSE. The time required for root-end preparation was recorded. The root apex samples were examined by scanning electron microscopy to assess root surface microcracks and marginal integrity. The remnants of gutta-percha on the cavity walls were evaluated using a stereomicroscope. Statistical analysis was performed using Student’s
t
-test and Wilcoxon rank-sum test (
P
<
0.05
). Usage of MSE with Jetip-2 significantly reduced preparation time from
99.8
±
6.8
s
to
32.4
±
1.0
s
(
P
=
0.009
), the number of microcracks from 42 to 13 (
P
=
0.036
), and the remnants of gutta-percha from 80% to 20% (
P
=
0.041
). Similar results were observed for AS3D with MSE. The heat softening of MSE was effective in cleaning gutta-percha, thus greatly improving the efficiency of the root-end preparation, thereby producing a root-end cavity with fewer microcracks and better marginal integrity.