Methods, systems, and apparatus, including medium-encoded computer program products, for computer aided design and manufacture of physical structures using subtractive manufacturing systems and techniques and a determined stock allowance include, in one aspect, a method including: obtaining a finishing toolpath specification for three dimensional (3D) geometry of a part; generating 3D geometry of a model of a semi-finished structure in accordance with a computer simulation of deflections experienced by a workpiece as stock material is cut from the workpiece using the finishing toolpath specification; creating a semi-finishing toolpath specification for the semi-finished structure; and providing the semi-finishing toolpath specification for use in machining the part by cutting away a first portion of the stock material using the semi-finishing toolpath specification to form the semi-finished structure, followed by performing a finishing operation of the semi-finished structure by cutting away a second portion of the stock material to form the part.