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Purpose: The purpose of this study was to present a more precise and objective way to assess the effectiveness of neuroendoscopic application in the treatment of middle cranial fossa arachnoid cysts. Methods: Between March 2009 and December 2012, 28 patients affected by middle cranial fossa arachnoid cysts were initially treated with endoscopic fenestration at the three spaces. The volumes of the cysts on MR images at the time of pre-op and 4 months after surgery were reconstructed by 3D Slicer and quantitatively calculated to compare the volumetric changes. The possible predisposing factors of surgical outcomes were analyzed as well. Results: All the models of the cysts were successfully reconstructed, and the mean volume of the cysts was 135.77 ± 90.43 cm before surgery and 93.08 ± 100.31 cm after surgery at 4 months follow-up ( t = 2.98, P = 0.006). The volumes of those two cases (7.14 %), presenting intracranial hypertension and ventricular dilation after surgery, were dramatically increased, whereas the others were decreased in 20 cases (71.43 %) or remained unchanged in 6 cases (21.43 %). There was significant difference on the age factor among the three result groups ( P = 0.001). Conclusions: The reconstruction of 3D for the assessment of the endoscopic fenestration outcomes is a feasible and precise way for clinical work. The variety of outcomes probably depends on age discrepancy. [ABSTRACT FROM AUTHOR]