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You learn to develop various coping skills, such as envisioning parts of yourself as the parts of the sex you identify as. You also do what you can to bring your body into alignment with your identity. I'm on testosterone therapy and that's really helped. I want surgeries, too, but that'll have to wait. For FtMs, we also bind our chests and use packers (to create the feel and appearance of a male groin). You just do what you can to cope.
It's not so much that as it is having to deal with strong negative feelings towards your own body because it's the opposite of who you are and all the insecurities that go along with that.