This achievement will be earned over at least 3 different missions, as none of these 3 knives can be found on the same mission. The Scalpel can be found during 'Terminal Hospitality' in several different rooms in the basement, while the Combat Knife can be found during 'Tubeway Torpedo' in the possession of Mikhail Bardachenko. The Kitchen Knife can be found during 4 different missions, 'The Gontranno Sanctuary', inside a parcel that you find, 'Anathema', in the kitchen, 'Invitation To A Party', in the lower levels of the building where the chef is and 'Tracking Hayamoto', in the room where the fugu fish can be found.
To unlock this achievement you must kill an enemy with each of the 3 knives, after obtaining them. Sneaking behind them, or maniacally slashing away at them will suffice. This choice is yours to make.