A magnetic apparatus having at least one magnetic shim situated between faces of two permanent magnets. The magnetic shim helps to make the magnetic field that is accessible between the two permanent magnets a more uniform field. The magnetic shim is constructed on a thinned semiconductor wafer, such as silicon, by photolithographically defining locations on the wafer where magnetic material, such as iron or iron-nickel materials, are deposited. The shim can additional have photolihographically defined coil regions, in which conductive material such as copper can be deposited. Current contacts are provided to allow currents to be passed through the coil regions. Protective layers can be deposited to protect the deposited metals from mechanical or environmental damage.