We have studied the alignment of liquid crystals (LCs) on homeotropic polymeric surface that is scanned using an atomic force microscope (AFM) tip by optical polarizing microscopy and computer simulation. The scanned areas on one substrate are 5 $mu extrm{m}$ ${ imes}$ 5 $mu extrm{m}$, 10 $mu extrm{m}$ ${ imes}$ 10 $mu extrm{m}$, and 20 $mu extrm{m}$ ${ imes}$ 20 $mu extrm{m}$ and this substrate is assembled to another substrate coated. with homeotropic polymer. The fabricated micro-LC cell using two substrates does not show any hysteresis and disclination lines inside the nano-rubbing areas, while changing voltage up and down. This indicates that the pretilt angle exists in the areas, thereby forming a hybrid LC configuration. From the experimental and computer simulation results, we can understand that the AFM rubbing clearly changes surface status of homeotropic alignment layer and causes the pretilt angle to an initial scanning direction.