One of the alluring aspects of liquid crystals (LCs) is their readily controllable self-assembly behavior, leading to comprehension of complex topological structures and practical patterning applications. Here, we report on manipulating various kinds of topological defects by adopting an imprinted polymer-based soft microchannel that simultaneously imposes adjustable surface anchoring, confinement, and uniaxial alignment. Distinctive molecular orientation could be achieved by varying the surface anchoring conditions at the sidewall polymer and the rubbing directions on the bottom layer. On this pioneering platform, a common LC material, (4'-n-octyl-4-cyano-biphenyl), was placed where various topological defect domains were generated in a periodic arrangement. The experimental results showed that our platform can change the packing behavior and even the shape of topological defects by varying the rubbing condition. We believe that this facile tool to modulate surface boundary conditions combined with topographic confinement can open a way to use LC materials in potential optical and patterning applications.