Cell handling is currently hindered by rudimentary-manufactured manipulators. Restrictive designs of glass pipettes and other micromanipulators limit functionality and often damage cells, ultimately resulting in lysis. We present a novel technique to design and mill conventional glass pipettes at specifically chosen angles and geometries. Focus ion beam milling by Ga+ ions yields extremely polished edges. Results from mouse embryo piercing correlate increased penetration rates with decreased pipette angle. Milled pipettes maintain structural integrity after repeated piercing. For the first time, the effects of unintentionally implanted Ga+ on embryo development are addressed. Optimum embryo development up to blastocyst stage after manipulation reveal little impact of residual implanted Ga+, suggesting biocompatibility and paving the way to introducing ion milling techniques in the biomedical device arena. The milling technique can be adequately tailored to specific applications and allows for mass production, presenting a promising avenue for future, increasingly demanding, cell handling.