Hi!
Take a look at the great pages of Paul Bourke: http://paulbourke.net/. You can find a matlab code for the distance of two lines in 3d in section "The shortest line between two lines in 3D" on page http://paulbourke.net/geometry/pointlineplane/.
You can as well use 2d coordinates with the third entry 0. Then you just check every line against the others.