A method of improving focused ion beam processing using a plasma ion source by reducing the number of energetic neutral particles impacting onto the work piece, comprising: applying energy to a gas in a plasma chamber to produce a plasma, the plasma chamber at a first pressure; extracting ions from the plasma chamber; forming the ions into an ion beam inside a focused ion beam column (200, 300); passing the ion beam into a sample chamber and focusing the ion beam onto a workpiece within the sample chamber using a focusing lens located inside the focused ion beam column; and processing a work piece using the focused ion beam, wherein the focused ion beam column comprises a first vacuum chamber (206, 306), a second vacuum chamber (210, 308), a first differential pumping aperture (209, 316), and a second differential pumping aperture (217, 318), wherein the second vacuum chamber is longer than the first vacuum chamber; extracting ions from the plasma chamber comprises extracting ions from the plasma chamber into the first vacuum chamber; and the ion beam passes from the first vacuum chamber to the second vacuum chamber through the first differential pumping aperture, and from the second vacuum chamber to the sample chamber through the second differential pumping aperture, while maintaining the first vacuum chamber at a lower pressure than the pressure in the plasma chamber and the second vacuum chamber at a lower pressure than the first vacuum chamber, wherein the second vacuum chamber being at the lower pressure than and longer than the first vacuum chamber reduces opportunity for formation of energetic neutrals, characterised in that a pressure in the sample chamber is maintained at a pressure greater than that of the second vacuum chamber. applying energy to a gas in a plasma chamber to produce a plasma, the plasma chamber at a first pressure; extracting ions from the plasma chamber; forming the ions into an ion beam inside a focused ion beam column (200, 300); passing the ion beam into a sample chamber and focusing the ion beam onto a workpiece within the sample chamber using a focusing lens located inside the focused ion beam column; and processing a work piece using the focused ion beam, wherein the focused ion beam column comprises a first vacuum chamber (206, 306), a second vacuum chamber (210, 308), a first differential pumping aperture (209, 316), and a second differential pumping aperture (217, 318), wherein the second vacuum chamber is longer than the first vacuum chamber; extracting ions from the plasma chamber comprises extracting ions from the plasma chamber into the first vacuum chamber; and the ion beam passes from the first vacuum chamber to the second vacuum chamber through the first differential pumping aperture, and from the second vacuum chamber to the sample chamber through the second differential pumping aperture, while maintaining the first vacuum chamber at a lower pressure than the pressure in the plasma chamber and the second vacuum chamber at a lower pressure than the first vacuum chamber, wherein the second vacuum chamber being at the lower pressure than and longer than the first vacuum chamber reduces opportunity for formation of energetic neutrals, wherein the focused ion beam column comprises a first vacuum chamber (206, 306), a second vacuum chamber (210, 308), a first differential pumping aperture (209, 316), and a second differential pumping aperture (217, 318), wherein the second vacuum chamber is longer than the first vacuum chamber; extracting ions from the plasma chamber comprises extracting ions from the plasma chamber into the first vacuum chamber; and the ion beam passes from the first vacuum chamber to the second vacuum chamber through the first differential pumping aperture, and from the second vacuum chamber to the sample chamber through the second differential pumping aperture, while maintaining the first vacuum chamber at a lower pressure than the pressure in the plasma chamber and the second vacuum chamber at a lower pressure than the first vacuum chamber, wherein the second vacuum chamber being at the lower pressure than and longer than the first vacuum chamber reduces opportunity for formation of energetic neutrals, characterised in that a pressure in the sample chamber is maintained at a pressure greater than that of the second vacuum chamber.