In the field of molecular robotics, many studies have applied cytoskeletal proteins and motor proteins for the actuation and deformation of molecular robots by confining compounds of the proteins in giant vesicles or microdroplets. Such confined cytoskeletal proteins exhibit orientational order of nematic liquid crystals, and the deformation of the molecular robots is controlled by singular points of the orientational angle, called topological defects. The aim of this chapter is to give theoretical tools for analyzing the behavior of topological defects to predict where the deformation of molecular robots starts. To this end, we introduce explicit formulae of nematic liquid crystals in arbitrary-shaped simply- and doubly-connected domains and then explain the method for determining defect positions by numerical minimization of the elastic energy of liquid crystals. Finally, we show some numerical examples of defect localization by asymmetric geometries and discuss the design principle of topographical guides for efficient control of topological defects.