Spatially characterizing and quantifying the brain electromagnetic response using MEG/EEG data still remains a critical issue since it requires solving an ill-posed inverse problem that does not admit a unique solution. To overcome this lack of uniqueness, inverse methods have to introduce prior information about the solution. Most existing approaches are directly based upon extrinsic anatomical and functional priors and usually attempt at simultaneously localizing and quantifying brain activity. By contrast, this paper deals with a preprocessing tool which aims at better conditioning the source reconstruction process, by relying only upon intrinsic knowledge (a forward model and the MEG/EEG data itself) and focusing on the key issue of localization. Based on a discrete and realistic anatomical description of the cortex, we first define functionally Informed Basis Functions (fIBF) that are subject specific. We then propose a multivariate method which exploits these fIBF to calculate a probability-like coefficient of activation associated with each dipolar source of the model. This estimated distribution of activation coefficients may then be used as an intrinsic functional prior, either by taking these quantities into account in a subsequent inverse method, or by thresholding the set of probabilities in order to reduce the dimension of the solution space. These two ways of constraining the source reconstruction process may naturally be coupled. We successively describe the proposed Multivariate Source Prelocalization (MSP) approach and illustrate its performance on both simulated and real MEG data. Finally, the better conditioning induced by the MSP process in a classical regularization scheme is extensively and quantitatively evaluated.