Lyotropic liquid crystals (LCs) are formed by suspensions of a wide range of anisometric particles, such as nanorods, colloidal disks, and macromolecular assemblies. At high concentration, the particles align with each other to reduce mutual exclusion volume and gain more translational entropy, resulting in a nematic orientational order. Controlling surface alignment of lyotropic LCs is critical in studying their physical properties and engineering them in applications, and is therefore a key next step of the research. The purpose of this study is to understand the surface anchoring energy of lyotropic liquid crystal due to nanopillar arrays on the substrate. We apply a magnetic field to distort the director field in the cell and observe the Frederiks transition. Applying a horizontal magnetic field in a vertically aligned cell will induce a competing factor of the free energy, where above a critical field, the director prefers to align with the magnetic field in the bulk. By measuring the threshold field as a function of cell thickness, we extract the extrapolation length associated with finite anchoring and determine quantitatively the anchoring energy using the bend elastic constant of the system. Our results will establish frameworks and techniques for characterizing surface anchoring in lyotropic liquid crystals and demonstrate the effectiveness of nanopatterned substrates in producing controllable homeotropic alignment.