A method of operating a focused ion beam column in the presence of a magnetic field from a magnetic electron immersion objective lens of a scanning electron microscope, comprising: directing a beam of electrons toward a sample, the electrons being focused by the magnetic immersion objective lens having a magnetic field that extends to the sample, directing a beam of ions toward a point on the sample surface in the presence of the magnetic field from the electron immersion objective lens; characterised by: shielding the ions within the focused ion beam column using a magnetic shielding material; and deflecting the beam of ions to compensate for the effect of the magnetic field on the ion beam, by dispersing the beam to form a spot on the sample surface that is less than 50% larger than the spot the beam would form in the absence of the magnetic field, the ion beam being directed to process the sample with sub-micron accuracy in the presence of the magnetic field; and where the deflecting of the beam of ions to compensate for the effect of the magnetic field on the ion beam includes deflecting the beam using at least two deflectors (534, 536, 538A, 538B), a first deflector deflecting the beam within the ion column to cause the ion beam to traverse an ion objective lens closer to its center than the ion beam would traverse without compensation in the presence of the magnetic field and a second deflector compensating for the magnetic field outside of the ion column to move the impact point of the ion beam to where the impact point would be in the absence of the magnetic field. directing a beam of electrons toward a sample, the electrons being focused by the magnetic immersion objective lens having a magnetic field that extends to the sample, directing a beam of ions toward a point on the sample surface in the presence of the magnetic field from the electron immersion objective lens; characterised by: shielding the ions within the focused ion beam column using a magnetic shielding material; and deflecting the beam of ions to compensate for the effect of the magnetic field on the ion beam, by dispersing the beam to form a spot on the sample surface that is less than 50% larger than the spot the beam would form in the absence of the magnetic field, the ion beam being directed to process the sample with sub-micron accuracy in the presence of the magnetic field; and where the deflecting of the beam of ions to compensate for the effect of the magnetic field on the ion beam includes deflecting the beam using at least two deflectors (534, 536, 538A, 538B), a first deflector deflecting the beam within the ion column to cause the ion beam to traverse an ion objective lens closer to its center than the ion beam would traverse without compensation in the presence of the magnetic field and a second deflector compensating for the magnetic field outside of the ion column to move the impact point of the ion beam to where the impact point would be in the absence of the magnetic field. shielding the ions within the focused ion beam column using a magnetic shielding material; and deflecting the beam of ions to compensate for the effect of the magnetic field on the ion beam, by dispersing the beam to form a spot on the sample surface that is less than 50% larger than the spot the beam would form in the absence of the magnetic field, the ion beam being directed to process the sample with sub-micron accuracy in the presence of the magnetic field; and where the deflecting of the beam of ions to compensate for the effect of the magnetic field on the ion beam includes deflecting the beam using at least two deflectors (534, 536, 538A, 538B), a first deflector deflecting the beam within the ion column to cause the ion beam to traverse an ion objective lens closer to its center than the ion beam would traverse without compensation in the presence of the magnetic field and a second deflector compensating for the magnetic field outside of the ion column to move the impact point of the ion beam to where the impact point would be in the absence of the magnetic field.