A machine for cleaning a head-disk assembly (HDA) of a hard disk drive (HDD) includes a nest that seals the HDA between an upper and lower portion during cleaning. An inlet port receives a gas and an exhaust port exhausts the gas and entrained particles. A shock drive delivers mechanical shocks to the nest and the HDA while the gas is flowing through the HDA. A blower may circulate the gas from the exhaust port to the inlet port. A filter may be coupled to the inlet port. The HDA nest may be movable along an axis of the mechanical shocks delivered by the shock drive. A blow tube may deliver gas to a screw hole and a coaxial vacuum tube may rest against a surface around the screw hole to encapsulate the blow tube during cleaning and remove the gas and particles from the screw hole.