My estranged mother's face still lingers in my mind's eye.
Literal
Separated mother's face [subject-が] still eye [in-に] remaining.
別れた母 is 'the mother I parted from' — possibly deceased or estranged. 目にのこっている means 'remains in the eyes' — an evocative way to say the image persists in memory. のこる (残る) is 'to remain,' and 目に places the memory in the visual sense. A poignant sentence about lingering memories.