Block-structured mesh generation techniques have been well addressed in the CFD community for automobile and aerospace studies, and their applicability to magnetic fusion is highly relevant, due to the complexity of the plasma-facing wall structures inside a tokamak device. Typically applied to non-linear simulations of MHD instabilities relevant to magnetically confined fusion, the JOREK code was originally developed with a 2D grid composed of isoparametric bi-cubic Bézier finite elements, that are aligned to the magnetic equilibrium of tokamak plasmas (the third dimension being represented by Fourier harmonics). To improve the applicability of these simulations, the grid-generator has been generalised to provide a robust extension method, using a block-structured mesh approach, which allows the simulations of arbitrary domains of tokamak vacuum vessels. Such boundary-aligned grids require the adaptation of boundary conditions along the edge of the new domain. Demonstrative non-linear simulations of plasma edge instabilities are presented to validate the robustness of the new grid, and future potential physics applications for tokamak plasmas are discussed. The methods presented here may be of interest to the wider community, beyond tokamak physics, wherever imposing arbitrary boundaries to quadrilateral finite elements is required.