много возможных путей
>>> mylist = [[3,4],[5],[6,7,8]]
>>> mylist[0] = [4]
>>> mylist
[[4], [5], [6, 7, 8]]
>>> mylist = [[3,4],[5],[6,7,8]]
>>> del mylist[0][0]
>>> mylist
[[4], [5], [6, 7, 8]]
>>> mylist = [[3,4],[5],[6,7,8]]
>>> mylist[0].remove(3)
>>> mylist
[[4], [5], [6, 7, 8]]
Выберите:)