In this paper, we shall consider an adapted finite difference preconditioning technique for radial basis function (RBF) method. This technique, for the system of equations that arises from solving Helmholtz equation with Dirichlet boundary conditions by RBF collocation method, is considered. We prove that the eigenvalues of preconditioned matrices are bounded for one and two-dimensional cases. We also show that RBF interpolating matrix can be well-conditioned by using appropriate number of polynomial bases in augmented term of RBF approximation. Numerical experiments show the efficiency and robustness of the preconditioning procedure, particularly when there are non-zero boundary conditions.