It's the words in the rest of the sentence that will tell you whether it was 'free' or 'tree' or 'three.' I'll give you an example. The Irish may have an accent which turns 'three' into 'tree.' But I always know they mean 'the number three' because the word 'tree' doesn't fit. If someone says, "There were tree of them," I know there were 3 people/things... because grammatically 'tree' does not fit. So try to work out what the word must be from the grammar or the general meaning. But don't worry... it takes time. Keep listening. Your brain will gradually sort it out.

because you need to improve your listening to realize the sounds you hear are different

In English, words that sound the same but have different spellings and meanings are called HOMONYMS. For example, the word FAIR has several meanings. 1- fair (white) - The Actress has fair, beautiful skin. 2 - fair (reasonable) - It wouldn't be fair to the others if she is paid more. Another example would be the words PEAR and PAIR (same sound) 1 - pear (fruit) - Pear is my favorite fruit. 2 - pair (couple) - My mom and dad have been married for 10 years. They are such a beautiful pair. That is why it is very important to read the full sentence so that you know the meaning of the word.

You can practice hearing the difference between those sounds with "minimal pairs" exercises such as these: http://www.englishclub.com/pronunciation/minimal-pairs.htm http://www.shiporsheep.com/

Hey, I used to have the same problem as you but in fact, the sounds are pretty different, just try to spend more time listening to people speaking English (watch movies, listen to music) and eventually you will see how different they are. Good luck!