You can define formulas (in Function Configs->Formulas) to modify how Mach3 moves. But you're FAR better off actually fixing the machine if you can.
For example, if your Y axis is tilted to the right by 0.003"/inch, you could enter a formula like this:
X = X - (Y * 0.003)
Y = Y
On a "straight" machine, when you tell Mach3 to move from Y0.000 to Y1.000, Y will move 1.000", and X will not move at all. On this hypothetical crooked machine, that same move will cause Y to move 1.000", but X will also move to the right, off-true, by 0.003", due to the error in the machine. Entering the above formula un-does this error. So, now when you command a move from Y0.000 to Y1.000, Mach will actually do a two-axis move, from X0.000, Y0.000 to X-0.003, Y1.000, "un-doing" the error in the machine.
Regards,
Ray L.