I think that there are two options here:
- renaming the main function and purpose of the machine to something else,
- renaming the standard "cut" in edit menu that would operate on clipboard.
Now, I suppose that the first way is not possible as "cutting" is probably something that is natural for the User that the machine does.
Renaming the other one would, on the other hand, be against a popular convention. But I think it may be a lesser sin in this case. You could rename this option to for example:
- move to clipboard,
- cut (to clipboard),
- copy and remove.
I know neither of these is perfect but sometimes using something imperfect is a direction to consider.
You should be aware of one thing, though. Remember that mistaking the clipboard meaning of "cut" for the physical meaning of it would trigger little to no consequences. In other words, if a User copies something to clipboard he will get confused but nothing bad will happen. It does not work like this the other way around — if they want to cut something to clipboard and trigger the machine operation then the consequences may be very frustrating.
Therefore, I would avoid using "cut" in general, replacing them with two options deriving from the same word:
for cutting to clipboard: one of the mentioned above, pointing directly the clipboard as a target of this action: "cut to clipboard",
for the main machine purpose I would use something that would convey the serious consequence of this action, for example "Perform cutting". I would support it with a confirmation popup that would explain User in simple words what is going to happen and ask User for confirmation with two buttons: Cancel and Perform cutting. You could add a checkbox [ ] never ask again in this popup, so that once Users learn which option does what, they will not need to confirm. However, this depends on if you are able to detect which Users are new and which are experienced using the machine.