If I’ve had sole custody for over 3 years but my daughter’s father is now filing for custody, what can I do?

Your first step is to make sure that you file a response to whatever motion he files to avoid any type of default judgment being entered against you.  Your second step is to review his motion and see what his basis is for requesting the modification.  The courts require that he have some basis.... not "just because I'm dad."  If there is no real basis listed and there have been no issues with you being the main conservator for three years, then you just need to stay focused on being a good mom.  While you wait on a final hearing, you can pull together information that would show the judge you are a good parent that has been successfully taking care of your daughter.  Essentially, you are pulling together a marketing summary for yourself-- but the items only need to be simple, direct, demonstrations of good parenting.  This could include things like:  child is current on shot record, child's grades in school are good, child participates in activities (with your or through school), you have a family doctor that sees the child on a regular basis, your daughter has adjusted well at day care.   One factor is not more important than the other--- but the general idea is to show the judge that you know what you are doing as a the parent, and you are doing your best to do it right.

If your ex's motion does have a basis that alleges some issue that you've had (for example:  a recent arrest for driving while intoxicated) or that your child has had, then you have a bit more work to do.  You will need to gather enough evidence to show that the child is back on track despite any "hiccups" in your parenting skillset.  If you want to retain custody of your daugther, make sure you take whatever steps are necessary to resolve the issue which is causing him to file his motion for custody.  The sooner you respond and fix the issue the better chance you will have a retaining sole custody-- because it shows you are motivated to take care of your child.