In this paper we analyze a long standing problem of the appearance of spurious, non-physical solutions arising in the application of the effective mass theory to low dimensional nanostructures. The theory results in a system of coupled eigenvalue PDEs that is usually supplemented by interface boundary conditions that can be derived from a variational formulation of the problem. We analyze such a system for the envelope functions and show that a failure to restrict their Fourier expansion coefficients to small k components would lead to the appearance of non-physical solutions. We survey the existing methodologies to eliminate this difficulty and propose a simple and effective solution. This solution is demonstrated on an example of a two-band model for both bulk materials and low-dimensional nanostructures. Finally, based on the above requirement of small k, we derive a model for nanostructures with cylindrical symmetry and apply the developed model to the analysis of quantum dots using an eight-band model.