This paper presents a novel approach for the identification of continuous-time systems. The proposed method is based on the projection of measured signals onto the finite-dimensional signal subspace whose basis is determined by the structure of the parameterized model of the target system. This structure-dependent basis enables us to estimate the specific parameter of the target system efficiently, and this aspect is especially useful in continuous-time system identification because parameters of such systems often correspond directly to physical parameters of the target system. Also, the proposed method can handle the closed-loop setting, which is frequently demanded in practical applications, as the specific structure of the model. The effectiveness of the method is demonstrated through a numerical example of closed-loop identification for an unstable magnetic levitation system with known physical constants.