Pruning for balcony plants, too late?

Last year we got dwarf plum and pear trees for our balcony. Both survived winter and came back to life this year. However I guess we missed pruning the trees in spring ; as a result there are branches shot up from low part of the tree. Looks not nice. Couple of questions

Can we prune the low branches this time of year?or when? 

Any help is much appreciated