One of the Egyptian capitals is named Thebes, a direct lift from the city-state of Thebes in Greece. And from looking at a map of ancient Egypt on Wikipedia, several of the cities continue to be known by a name using the -polis suffix (e.g. Herakleopolis), a very Greek name for a city, but highly unlikely to also be an Egyptian name. Why did the Greeks have such an interest in this foreign culture, besides their enigmatic pyramids? And why didn't other conquerors of Egypt like Persia also have this interest?
Apart from the threads mentioned by /u/Dinocrocodile I would be remiss not to point out that Egyptian Thebes probably is not, as you put it "a direct lift from the city-state of Thebes in Greece." First of all, "hundred-gated Thebes" appears already in Homer, who preserves the (probably) original form (at least in Ionic), Θήβη alongside Θῆβαι for the Boeotian seven-gated city, likely from *Thēgʷā. Probably hundred-gated Thebes was originally called such either for the nearby area called Čēme in Coptic, or from the Karnak temple complex called ta-opet. It's hard to tell with Greek transliterations of Egyptian, but it's a familiar pattern (c.f. Memphis, which had several names over the centuries but whose Greek name derives from the nearby pyramid complex to Pepi I, Mn-nfr-Pjpj). Almost certainly the similarity between the Egyptian and Boeotian cities' names occurred to Greek speakers early on, and drove further association between the two, but it was likely not originally just a transplanting of the Boeotian town's name.
Since /u/TarvosTrigaranus mentioned the Hellenistic period, you might be interested in the FAQ on Hellenistic Egypt which has a bunch of good entries.