when you use them as "BUT", they are no much difference. However 不过 has one more meaning, can not be better. normally use in the end. like "再好不过了"

可是 = 但是 = but 不过 = however

不过 bùguò (1) [cannot be better] ——用在形容词性的词组或双音形容词后面,表示程度很高 那就再好不过了 (2) [but;however;only] ——作连词,表示转折, 病人精神还不错,不过胃口还不好 (3) [only;just;merely;nothing but;no more than]∶副词,指明范围;只, 仅仅不过是个小孩子 可是 kěshì [but]——连接分句、句子或段落,表示转折关系,常和前面的“虽然”相呼应;先由“虽然”引出一层意思,后用“可是”一转,引出相反或不一致的意思。相当于“但是” 他虽然有病,可是仍继续工作