At a 7 week scan our fetus only measured 3.5 mm. is this cause for concern?

Probably not: A 3.5 mm crl would indicate a fetal gestational age of 5wks 6dys. Since clinical estimates of dates are frequently a bit off this is not a big deal. It probably was a little early to clearly see fetal heart activity. A repeat scan in 2 weeks that shows appropriate interval growth and definite fetal heart activity will confirm fetal life and the earlier dates. Good luck!