A system and methods are provided for removal of undesired portions of a fruit or vegetable, such as removal of calyxes from strawberries before they are flash frozen. An automated process for high-throughput fruit or vegetable calyx removal includes a loading system, an identification system, and a removal system. The loading system is configured to transport the fruit or vegetable through the automated process. The loading system may also orient the fruits or vegetables along an axis of the fruit and or align the fruit or vegetables in a desired pattern, orientation, and/or arrangement. The identification system is configured to locate the calyx and determines calyx position data and an optimal cutting path for individual fruit. The removal system uses data received from the identification system to separate the calyx from the fruit or vegetable.