I was suffering from eczema, and during those time I scratched my skin so much that I now have a lot of dark marks on my skin. Can they be removed?

Can be improved. Most likely they can be improved, but it is hard to know exactly what will be the best solution. Possible treatments include some topical creams or perhaps an erbium laser treatment like fraxel. Unless the marks are very severe, surgical removal will not be a very good option. Seek out a knowledgeable dermatologist or plastic surgeon.
Improved maybe. If you have pigmentation changes from trauma (scratching) there may be treatments that can improve things. Honestly i doubt that they will be able to be completely removed.
It depends . This is most likely something we call post inflammatory hyperpigmentation. This may improve with time. A topical hydroquinone may be prescribed to help lighten. Always best to avoid sun as this can make it worse.