An inverted mass hierarchy in the squark sector, as in so-called "natural supersymmetry", requires non-universal boundary conditions at the mediation scale of supersymmetry breaking. We propose a formalism to define such boundary conditions in a basis-independent manner and apply it to generic scenarios where the third-generation squarks are light, while the first two generation squarks are heavy and near-degenerate. We show that not only is our formalism particularly well-suited to study such hierarchical squark mass patterns, but in addition the resulting soft terms at the TeV scale are manifestly compatible with the principle of minimal flavour violation, and thus automatically obey constraints from flavour physics.