In this paper, we solve two problems in linear systems theory: the computation of the inner-outer and spectral factorizations of a continuous-time system considered in the most general setting We show that these factorization problems rely essentially on solving for the stabilizing solution a standard algebraic Riccati equation of order usually much smaller than the McMillan degree of the transfer function matrix of the system, The proposed procedures are completely general, being applicable for a polynomial/proper/improper system whose transfer function matrix could be rank deficient and could have poles/zeros on the imaginary axis or at infinity. As an application we discuss the extension to the case of rational matrices of the complete orthogonal decomposition of a constant matrix. Numerical refinements and examples illustrating the proposed approach, are discussed in detail.