This paper reports the development and testing of atomistic models of silica MCM-41 pores. Model A is a regular cylindrical pore having a constant section. Model B has a surface disorder that reproduces the morphological features of a pore obtained from an on-lattice simulation that mimics the synthesis process of MCM-41 materials. Both models are generated using a similar procedure, which consists of carving the pore out of an atomistic silica block. The differences between the two models are analyzed in terms of small angle neutron scattering spectra as well as adsorption isotherms and isosteric heat curves for Ar at 87 K and Xe at 195 K. As expected for capillary condensation in regular nanopores, the Ar and Xe adsorption/desorption cycles for model A exhibit a large hysteresis loop having a symmetrical shape, i.e., with parallel adsorption and desorption branches. The features of the adsorption isotherms for model B strongly depart from those observed for model A. Both the Ar and Xe adsorption branches for model B correspond to a quasicontinuous pore filling that involves coexistence within the pore of liquid bridges and gas nanobubbles. As in the case of model A, the Ar adsorption isotherm for model B exhibits a significant hysteresis loop; however, the shape of the loop is asymmetrical with a desorption branch much steeper than the adsorption branch. In contrast, the adsorption/desorption cycle for Xe in model B is quasicontinuous and quasireversible. Comparison with adsorption and neutron scattering experiments suggests that model B is too rough at the molecular scale but reproduces reasonably the surface disorder of real MCM-41 at larger length scales. In contrast, model A is smooth at small length scales in agreement with experiments but seems to be too ordered at larger length scales.