► Hierarchical refinement of NURBS offers full analysis suitability, straightforward implementation and simple generalization to 3D. ► We first explore local hierarchical refinement for adaptive NURBS-based IGA. ► We then combine the B-spline version of the FCM and hierarchical refinement for a seamless design-through-analysis integration of 3D T-spline surface based models. We explore hierarchical refinement of NURBS as a basis for adaptive isogeometric and immersed boundary analysis. We use the principle of B-spline subdivision to derive a local refinement procedure, which combines full analysis suitability of the basis with straightforward implementation in tree data structures and simple generalization to higher dimensions. We test hierarchical refinement of NURBS for some elementary fluid and structural analysis problems in two and three dimensions and attain good results in all cases. Using the B-spline version of the finite cell method, we illustrate the potential of immersed boundary methods as a seamless isogeometric design-through-analysis procedure for complex engineering parts defined by T-spline CAD surfaces, specifically a ship propeller and an automobile wheel. We show that hierarchical refinement considerably increases the flexibility of this approach by adaptively resolving local features.