I took over a franchise where the prior owner has a bunch of marginal talent on the 40 man roster. Is the only way to remove them from the 40 to waive them? I have other players I need to protect from the Rule 5 draft. What are my options here? Try to trade some and get players in return? Thanks in advance.

Waive them, then remove the ones who clear.  If they're truly marginal talent, chances are they won't get claimed.

If they are making MinL salary and they have options left, odds are they will be claimed, since they can be assigned to the the MinL by the team that claims them.

If they don't have options, anyone claiming them will have to assign them to their ML team. So there's much less chance they'll be claimed.

If they are AAAA talent, it's not worth worrying about. You'll have chances to claim similar players or pick them up as FAs at the start of the season.

If you need to make room quickly, designate them.   Immediately removes them from the 40. 

also, if they have options you don't have to expose them to waivers.  just designate without waivers are assign back to minor leagues.  They would be elgible to be selected in Rule 5, but you don't have to worry about someone claiming them through waivers.  If they don't have options, you'll have to expose them to waivers to get them off the 40 AND keep them.