First of all, thanks of all for your responses and tips and sorry for my delayed responses!
A little bit of history about these trees. They started spontanously growing when after I spitted out the seed into a pot with some soil. I separated all the seedlings.
The apple trees were "Granny Smith", for the lemons (identified through the leaves, they could have been grapefruit or oranges as well). No idea of the root stock.
As discussed in another topic, I'm fighting powdery mildew on my apple trees they cought whilst they were in their pots inside.
They are now out on my small balcony they get I guess a full day of sun. The lemon trees are inside as I don't have enough space on the balcony and I'm afraid they might die in winter. However they are close to a windows so I hope they get enough sun.
I pruned one apple tree early but he was never thin stemmed. I am afraid of pruning my apple trees as they are infected with powdery mildew an infect the tree deeper. Is there the risk.
How far can I prune my lemon tree? Down to the woody part or should I leave some of the green stem on? Thanks for your help!!!!