The most "handmade" shoes you can commonly buy are entirely handmade apart from the stitching on the upper. These will be described as bespoke shoes, or custom shoes, or handsewn shoes.
They are made to order and are individual to each customer.
It is possible to stitch a pair of uppers by hand, but it is very rarely done and looks 'agricultural'.
Almost any shoe you buy ready to wear will involve machines in a factory. The quality can vary hugely, from the best (Edward...