The Empirical Interpolation Method (EIM) and its generalized version (GEIM) can be used to approximate a physical system by combining data measured from the system itself and a reduced model representing the underlying physics. In presence of noise, the good properties of the approach are blurred in the sense that the approximation error no longer converges but even diverges. We propose to address this issue by a least-squares projection with constrains involving a some a priori knowledge of the geometry of the manifold formed by all the possible physical states of the system. The efficiency of the approach, which we will call Constrained Stabilized GEIM (CS-GEIM), is illustrated by numerical experiments dealing with the reconstruction of the neutron flux in nuclear reactors. A theoretical justification of the procedure will be presented in future works.