This sounds a lot like on of my favourite military fantasy series, The Corean Chronicles, LE Modesitt Jr.
The books centre on Alucius, from his mothers pregnancy until he reaches manhood. He becomes a nightsheep farmer with his grandfather, which is the province of people who have special, though secret, magical abilities, Talents. He is drafted into the militia when he comes of age. He becomes a scout. He destroys a new weapon of the enemy's that shoots purple crystal spike things. He is captured by the enemy and forced to join their militia.
The Immortal Matrial, ruler of the enemy he now fights for is indeed an alien. He doesn't realise this, but he realises she has control over everything in a magical sort of way and he kills her, escapes and takes other captives with him. Ends up moving up in the ranks of his original militia.
In one of the other two books he does wake up in a tower which is in the city of the Soarers, an ancient race, the original inhabitants of the planet, they are described kind of like fairies, all floaty and green glowing (or at least green auras).
There are special mirror tables that can be used to view things far away and also be used as portals. The "aliens" once lived on the planet, they created those mirror tables, they are trying to return to take over the planet.
There is no story about his daughter. Though he does have a child near the end, his wife becomes a main character along with him near the end too. However after the second trilogy, so book 7 in the entire series, the story does become about the Lord-Protectors Daughter (that's what it is named actually). However, that book is set before Alucius' time and after the time period of books 4-6.