The church legally must process resignation requests for under-18s. They require these to be signed by the legal guardian(s) who have custody of a child.
In general, the process is the same as resigning an adult member regardless of whether or not the child was ever baptised.
Some parents and guardians find it helpful to submit a resignation for their child and wait until the child is no longer visible on LDS Tools and the ward list before submitting their own resignation. This is not necessary, but may provide you some reassurance.