Shielding can be a very deep topic but basically you can
1: Shield the wires (hopefully very short and not near high power/motor wires, can be challenging to debug/verify)
2: Use differential signals, routed together, ideally with a twisted pair
Differential is definitely the way to go, if your motor controller has separate D+/D- and S+/S- signals you should use them. Differential basically means one line will go high, the other will go low to represent a "1", and they will reverse to represent a "0". Doing it this way means that any electrical noise on the wires due to power supply noise, EMI, magnetic fields, etc. will affect both lines together.
Because differential signaling uses the voltage difference between the lines, most noise will not alter the signal.
For more info, lookup "Common mode noise" and "differential signaling".
If you do use differential signals, make sure to use either twisted pair (hacked Ethernet cables work well) or are routed very close together.