We present a novel approach to 3D structural shape optimization that leans on an Immersed Boundary Method. A boundary tracking strategy based on evaluating the intersections between a fixed Cartesian grid and the evolving geometry sorts elements as internal, external and intersected. The integration procedure used by the NURBS-Enhanced Finite Element Method accurately accounts for the nonconformity between the fixed embedding discretization and the evolving structural shape, avoiding the creation of a boundary-fitted mesh for each design iteration, yielding in very efficient mesh generation process. A Cartesian hierarchical data structure improves the efficiency of the analyses, allowing for trivial data sharing between similar entities or for an optimal reordering of the matrices for the solution of the system of equations, among other benefits. Shape optimization requires the sufficiently accurate structural analysis of a large number of different designs, presenting the computational cost for each design as a critical issue. The information required to create 3D Cartesian h-adapted mesh for new geometries is projected from previously analyzed geometries using shape sensitivity results.Then, the refinement criterion permits one to directly build h-adapted mesh on the new designs with a specified and controlled error level. Several examples are presented to show how the techniques here proposed considerably improve the computational efficiency of the optimization process.