This research investigates on the numerical methods for computing the greatest common divisors (GCD) of two polynomials in the orthogonal basis without having to convert to the power series form. Previous implementations were conducted using the Gauss Elimination with partial pivoting (GEPP) and QR Householder algorithms, respectively. This work proceeds to seek for a better approximate solution by comparing the results of the implementations with the QR with column pivoting (QRCP) algorithm. The results reveal that QRCP is as competent as the GEPP algorithm, up to a certain degree, giving a reasonably good approximate solution. It is also found that normalizing the columns of the associated coefficient matrix slightly reduces the condition number of the matrix but has no significant effect on the GCD solutions when applying the GEPP and QR Householder algorithms. However equilibration of the columns by computing its ∞-norm is capable to improve the solution when QRCP is applied. Comparing the three algorithms on some test problems, QR Householder outperforms the rest and is able to give a good approximate solution in the worst case condition when the smallest element of the matrix is 1, the entries ranging up to 15 digits integers.