Could medications that i take prior to implantation harm the baby?

Preconception meds: The research data is pretty spartan. Off the top of my head I would say methotrexate (psoriasis, cancer) and possibly because they deplete folate (folic acid) which can lead to neural tube defects. Obviously, any sufficiently large dose of progesterone can block implantation. Klonopin is Category D (some fetal risk) (1st but mainly 3rd trimester) The studies don't show high risk but the risk isn't zero.

Depends on the med: If the medication affects your uterine lining (endometrium), it can affect the ability of the pregnancy to implant. If the medication has a long half-life, meaning that it stays around in your body for a long time, it can potentially affect the fetus. However, it's rare for a medication to stay around the system for that long.