In FIB processes, the bombardment of positively charged Ga+ ions to the surface of an insulator can cause sample charging. The high energy ion bombardment in the sample can accumulate into several thousand volts of charge which can result in large craters and local melting due to electrostatic discharge.
On the other hand, during FIB milling, the main ion kinetic energy is eventually converted to heat, with only a small portion stored as defects in the sample or emitted as energetic particles or radiation.  The maximum temperature reached in the sample can be given by, 
T = P/(κaπ) -----------------------------------
P - The beam power P,
κ - The sample thermal conductivity,
a - The radius of the circular ion beam profile on the sample surface.
For commercial FIBs, the values of P/a are between 1 W/m and 1000 W/m, and thus the temperature rise can range from negligible for samples with good thermal conductivity to huge for poor conductors.  For instance, for Si (κ = 148 W/mK) the temperature increase is <2 °C even for the most extreme beam conditions.
Note that beam heating can be eliminated by placing the samples in good contact with a heat reservoir.
 L.A Giannuzzi, F.A. Stevie, Introduction to Focused Ion Beams: Instrumentation, Theory, Techniques, and Practice (Springer, New York, 2005).
H.S. Carlslaw, J.C. Jaeger, Conduction of Heat in Solids (Oxford University Press, Oxford, UK, ed. 2, 1959) p. 264.
 C. A. Volkert and A. M. Minor, Focused Ion Beam Microscopy and Micromachining, MRS BULLETIN, 32, 389 (2007).