1. A method of aligning a first surface with a second surface, such that P(x i ,y i ,z i ) is any point on the first surface and Q(x′ i ,y′ i ,z′ i ) is any point on the second surface, said first surface and said second surface being separated by a first-degree separation, a second-degree separation, and a third-degree separation, including the steps of: minimizing the first-degree separation by the steps of: selecting at least one feature point form each of the first surface and the second surface; adjusting the coordinate of the second surface to minimize the distance between said at least one feature point of each of the first surface and the second surface to be below a predetermined threshold value θ; minimizing the second-degree separation by the steps of dividing the first surface into a plurality of first zones, each first zone having at least one first coordinate defining said first zone; dividing the second surface into a plurality of second zones, each second zone having at least one second coordinate defining said second zone; for the plurality of first zones, repeating the steps of: a) obtaining distances between the at least one first coordinate and each of the plurality of second zones; b) comparing the distances obtained in step a) to determine a pair of corresponding zones on the first and the second surfaces having a minimum distance obtained in step a); until all zones on the on the first and the second surfaces are paired; determining the distances between each pair of corresponding zones on the first and the second surfaces; obtaining a summation of the distances between each pair of corresponding zones; adjusting the coordinate of the second surface to minimize the summation of the distances between each pair of corresponding zones to be below a predetermined threshold value ε; minimizing the third-degree separation by the steps of: minimizing a transfer matrix T to be below a predetermined threshold value λ by adjusting at least one pair of parameters along a direction, one of said parameters relates to translation and the other parameter relates to rotation along the direction.