Micro tomography images allow obtaining fully detailed microstructural descriptions of heterogeneous materials and structures. To evaluate the effects of local gradients induced by the boundary conditions, it might be of interest to perform Direct Numerical Simulations (DNS) of such structures. In this paper, a multiscale method is developed to perform DNS on large, non-periodic linear heterogeneous structures with arbitrary boundary conditions and which can be performed in a classical Finite Element context. The method uses off-line calculations on subdomains that do not require to be periodic. Then, direct segmented images of the full 3D structure can be used directly without simplification. The novelty here is the use of non-periodic subdomains to decompose non-periodic heterogeneous structures and the possibility to use a coarse mesh which does not conform to the boundaries of the subdomains. As a result, the full-field finite element problem can be solved on the basis of the coarse mesh only, reducing drastically the computational costs. The accuracy of the method is analyzed on benchmarks and applications on large heterogeneous structures such as arising from 3D microtomography images are presented.