Some boots are designed to allow heat moulding for a perfect fit. This process will relieve any small areas of pressure felt on your feet while skating, particularly around the ankles and toes.
Heat moulding cannot typically resolve skates being too large.
Where you have specific issues with your feet, punching may be required on a specific area. This process is used where heat moulding alone isn't likely to completely solve the issue, or where heat moulding isn't an option.