A method to represent complex flow features as geometric entities, using the medial axis for the purpose of generating flow-feature aligned meshes, is presented. These geometric entities are embedded into the domain to influence the generation of unstructured quad-dominant surface meshes in two and three dimensions. The resulting high-quality feature-aligned surface meshes can locally mimic the attributes of a structured grid. This paper also presents a method to extrude shock-aligned quad-dominant surface meshes beyond the boundary layer to cover the extent of transonic shock waves. The process provides a means to embed a high-quality hex-dominant mesh block, aligned with the transonic shock wave, into a hybrid volume mesh for viscous computations. Inclusion of the aligned mesh block is shown to enhance the ability of the hybrid mesh to resolve the shock wave, and thus, improve the numerical solution.