1. Skopje
Even skopje its a changed name since it was originally founded by
Dardanians as Skupi.
2. Debar
Another changed name. The first recorded document mentioning Debar is
the map of Ptolemy, dating around the middle of the 2nd century, in
which it is called Deborus.
3. Delcevo
Wikipedia says during Ottoman times it was called "Sultania" or
"Sultaniye" and later Carevo Selo. The town was renamed its present
name Delčevo in 1950.
4. Kavadarci
The name Kavadarci is derived from the Greek word, “Kavadion” which
means “cape made from a valuable material”. The citizens of Kavadarci
being manufacturers of this material, the first recorded use of this
name was during the first half of the 19th Century.
5. Kicevo
The original ancient Macedonian name was Uskana and was mentioned for
first time in the reign of Perseas, king of Macedon during the Third
Macedonian War (171-169 BC). Another ancient Macedonian name changed
by Skops.
6. Negotino
Negotino was known under the name of Antigoneia. It was founded by the
Macedonian king Antigonus II Gonatas, in the period between 278–242
BC.
7. Gostivar
>From wikipedia: "Possibly the first mention of the town was made by
the Roman historian Livy. He records how during the Third Macedonian
War the King of Macedon Perseus at the head of 10000 men, after taking
Uskana (Kicevo), attacked Drau-Dak, today Gostivar.
8. Ochrid
Wiki: Historical names include Dyassarites which is of Illyrian
origin , and the Greek names Lychnidos (Λύχνιδος), Ochrida (Οχρίδα)
and Achrida (Αχρίδα), the latter two of which are still in modern
usage.
9. Valandovo
Wiki: Evidence of life can be found beginning in the 10th-7th
centuries B.C. There is a settlement known as Mal Konstantinopol
(Small Constantinople) dating from Roman times, and the life in the
Middle Ages is marked by Marco’s Tower. In the vicinity of the town
there are also two very important archeological sites – The Isar
Marvinci and the knowledge experts have on the existence of the
ancient city Idomene.
10. Prilep
I have read once its ancient name was Parembole and certainly it was a
Greek name.
11. Demi Hisar
It was known as SideroKastron when Greeks lived there. Later in
Ottomantimes, the name was changed in to ”Demir Hisar” which in their
language means ‘’ Iron Mountain’’. Another original greek toponymy
renamed.
12. Demir-Kapija
Demir-Kapija is a place already mentioned in Classical times under the
name of Stenae (Greek for gorge). In the Middle Ages it was known as a
Slav settlement, under the name of Prosek, while today's name
originates from the Turkish reign, meaning "The Iron Gate".
13. Štip
Originally an ancient Macedonian city called astibo which was renamed
later to Štip.