There are several technique that can be used to measure the FIB beam size. It used to be a top topic in literature. See these articles:

Article Beam‐size measurements in focused ion beam systems

Article Measuring the beam size of a focused ion beam (FIB) system

All new FIB have these answers in their catalogue. Just look under focused ion beam diameter measurements

Greeting,

I am rather familiar with early methods like measurement the width of a sputter- etched on gold film and observing the chemically etched pattern of implant damage in the substrate. The line widths of such etched patterns correlate to beam diameter. By those method it’s impossible to measure the beam size during the implantation processes.

Knife edge method is the other method which has been used to measure FIB diameters. The main idea of this method is detecting signal-intensity variation in FIB scanning through the use of a sharp edge.

One of the common method is to expose the substrate after coating it with a PMMA resist. The developed resist pattern reflects the shape of the beam.

Which method are you using in your equipment?

You can correlate and use DOE. To optimize your condition