I'd make something that is approximately 4cm apart in maya, but when I make the stl file through blender it less than 1cm entirely.
I need this fixed as I dont want to use more software packages.
Is this really a Cetus problem? Maybe the workflow is generating an STL file with the wrong scale?
I have created models in other packages and the scaling in Cetus has been correct.
If Maya can import an stl file, if the generated stl file is the correct size it should match the original model.
The STL file format doesn't have information on real-world size, just a unit-free size, afaik. Convention is to use mm for that, but perhaps Maya is exporting it at a different scale. One thing you could do is download a 20x20x20mm calibration cube from thingiverse (there's a few on there), load it in Maya and look at the scaling. Then compare it to what you're doing.