By system, I assume you mean general circulation. Evidence of medication and drug use can be seen in your hair for months, well after it is gone from blood and urine. That only takes a few days depending on the precision of the test, amount used, frequency of use, etc..
Marijuana hasn't been studied specifically for its ability to cause birth defects, but generally it is not associated with any specific birth defect. Other drugs, such as cocaine can be very dangerous to mother and baby because of blood pressure and blood flow effects that can cause strokes, and interrupt normal fetal and placenta development leading to birth defects, retardation, fetal death and maternal hemorrhage.