Most probably you are referring to conducted noise ( via common ground loops / Power supply ). Radiated noise if you are sure about it, will need a redesign of the enclosure - or atleast the protion that contains the MCU. But I am sure that may not be the issue. As a matter of routine check, verify the following :

1. Is the power supply to the MCU common with any other high power switching load - like solenoids/ power relays etc. If so you would do well to provide a sepearte secondary winding for the MCU power supply.

2. Is there a possiblity of any field sensors / push buttons getting directly wired to the MCU port pins? If yes, this is sure problem area. Isolation of port pins is a must for industrial applications.

3. If you are using external interrupts, then be sure that those cable are adequately shielded before being connected to the INTO / INT1 pins. If you can isolate this, do so.

4. Are you sure all coils ( of relays / solenoids etc ) have snubbers or reverse diodes. Dont underestimate these - failure to provide these can be potentially frustrating and worse still they can strike when least expected.

5. Preferable the MCU ground be floating - if you can avoid linking it with power ground - best.

Actually the above were points that had to be done before we could succesfully interface a MCU to control a variable speed AC drive - the king of all noise generating items !! Today we have no problem.

The above are just guidelines - you know what is best.

Thanks

Raghu