Last July I travelled from Thessaloniki to Sofia to Plovdiv. As there are no international trains in Greece any more, this is difficult. I took a city bus from airport to the Thessaloniki bus station. From there I took a bus to Serrai. I got on another bus to Sidirokastro. From there i took a taxi to the Bulgarian border. Just across, you can catch a train to Sofia from which you can take train to Plovdiv. I am sure there are trains from Athens to Thessaloniki.
I would really recommend using busses - they are privately owned , they are relatevely cheap and they offer a faaar better and more secure service than trains!
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