If a species has a vestigial anatomical structure that it no longer uses, it may or may not disapear through natural selection.
Evolution is based on four mechanisms :
- natural selection
- sexual selection
- genetic drift
A no longer used structure can disapear if a mutation makes it to. Then, if it confers a selection advantage (natural or sexual), then individuals without that structure will survive and / or reproduce better than the other. The mutation will spread among the population and structure may finally disapear.
If it does not confer benefit the individual nor decrease it's chances of survival or reproduce compare to others, mutation may or may not be conserved and so for the structure.
Genetic drift can accelerate disapearance of a structure, especially if the population is really small, even if it does not confer any advantages to the individuals. The mutation can rapidly spread through the population just by chance.
For example, in human body, the appendix is no longer used but still remains. It's absence does increase chance of survivol nor is attractive to sexual partners, so it doesn't imply natural or sexual selection structure. Genetic drift may or may not randomly make it disapear one day, no one knows.