If by Turkicised, OP, you simply mean “made to adhere to Turkish phonotactics, and often Vowel Harmony”, the answer is indeed most if not all. To add to Pierrick Jaouen’s examples, stin Poli (to the City) > İstanbul, is Nikea (to Nicaea) > İznik, Oinoë (mediaeval Greek /ynoi/) > Ünye, Ikonion > Konya, Kaisareia > Kayseri. And so on.
Not all towns have kept their old names of course. Rhaedestus was originally Rodosçuk in Turkish; it turned into Tekfurdağı “Byzantine Lord’s mountain” and then Tekirdağ after the 18th century. Some town names have been translated, though the two examples I thought of turn out to have been translated from Turkish into Greek, rather than vice versa: Κιρκλαρελί (contra what is said in Kırklareli: “Forty Churches” is not a Byzantine name) and Gümüşhane (the Pontic Greek name is Kanin, Argyropolis is learnèd).