Noise In The Laser System

It will be radiated or conducted.
An isolation transformer will do nothing to reduce noise, it will go straight through any transformer.
Some filtering on the incoming mains would be a good start.
Analysing the noise is also a good idea, is it a fixed frequency? Pulsed? Regular?Random? in sync with anything operating in the vicinity?
Are we talking megawatts, milliwatts or what watts?
You post is pretty much devoid of any useful info' so it's hard to comment further.
Del

To avoid the forum needing to play a game of "20 Questions" in order to assist, please provide a full description of the noise, its characteristics, and the behaviour of the equipment while it is both present and absent. This will enable a quicker solution to be found than going down the "20 Questions" route, and thereby eliminate the trivial possibility of a mouse having made a home inside it, for example, far earlier.

I bet its actually a little light bulb that blinks...