This paper constitutes the numerical counterpart of the mathematical framework introduced in Part I. We address the problem of flutter analysis of a coupled fluid-structure system involving an incompressible Newtonian fluid and a reduced structure. We use the Linearization Principle approach developed in Part I, particularly suited for fluid-structure problems involving moving boundaries. Thus, the stability analysis is reduced to the computation of the leftmost eigenvalues of a coupled eigenproblem of minimal complexity. This eigenproblem involves the linearized incompressible Navier-Stokes equations and those of a reduced linear structure. The coupling is realized through specific transpiration interface conditions. The eigenproblem is discretized using a finite element approximation and its smallest real part eigenvalues are computed by combining a generalized Cayley transform and an implicit restarted Arnoldi method. Finally, we report three numerical experiments : a structure immersed in a fluid at rest, a cantilever pipe conveying a fluid flow and a rectangular bridge deck profile under wind effects. The numerical results are compared to former approaches and experimental data. The quality of these numerical results is very satisfactory and promising.