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Malta Enterprise have a unit specifically for this. I used their services and they were very helpful. They can guide you and also help you tap on tax schemes and other grants. Check their website . Tel no. (+ 356) 2542 0000. Email info@businessfirst.com.mt​

I used to recommend businessfirst a lot, but honestly the last couple of visits ( I regularly visit different offices helping people with translations), I was disappointed. Sometimes the people working there are not very well informed and not really able/willing to offer advice, just push the paperwork to fill. Couple of years ago when I visited the first time, they were much more pro-active, offering advice as well, not just he paperwork. Maybe it was just back luck, but the last couple of times applicants had to go back couple of times, as something always was missing. The procedure is very simple, you can easily do it on your own. You will have to register with ETC as a self-employed ( a very simple two-page form with basic information). Assuming that you already have an residence card and you worked in Malta before (so you have social security number and tax number). You also will need a VAT number, what you can request at the Birkirkara VAT office or download the documents from their website and send it by post.
Good luck!

Thank you both for your replies.. I'll give the business center a go and see how the seem and keep looking for another few options. Good to know though. Thanks

It wont be quick - it's malta everything is ridiculous, but its not onerous. I used ccpsmalta.com and have been happy

WH Partners. They are not cheap (although, not overpriced, in my opinion), but they have been reliable and responsive, and they get things done pretty quickly.

I can refer a personal friend to advise you on this if you would like me to PM?