The way I like to play against Samus with Marth is to slow down the pace of the match a lot. Once you get Samus in the air, go berserk but make sure you tip all of your aerials or she will combo break with a nair or something.
When I'm on the ground and so is Samus, I jab through all of her missiles (jab seems to be the fastest and you don't have to be in the air... samus seems to like it when you forward air her missles). I then approach using spaced down tilts or forward tilts. Space down tilt so it will be just out of poking range (so it won't hit her). This covers a few of Samus's movement options. If you space like that, I'm pretty sure she can't hit you with anything.
Once you are in that specific range, start alternating down tilts and forward tilts. The forward tilt has a tad bit more range than dtilt, and it pressures her shield. By doing this, she is trapped in her shield from the ftilt's range, and trapped in zone where she can't hit you because of the dtilt's speed. If she decides to grab, your ftilt will out speed it. If she tries to jump, you can fsmash and it will most likely be a tipper.
Also, you want to be pressuring like this when she is near the ledge, since she doesn't have any space to run away. If you are not in this position, you can keep up with her by simply walking and still keep your perfect spacing.
Since you are covering so many of her options, she will be taking hits, and eventually you will get a tipper ftilt or fsmash, and once you get her off stage or in the air, you can really start doing damage.
I get most of my kills from side-b -> uptilt or just by smart edgeguards using bairs and such.
I hardly approach her from the air if she is on the ground because it seems like she has too many options to cover your approaches. You can tip your aerials so she can't crouch cancel, but then she can just wavedash out of your tipper range and hit you.
I also like to use counter a lot in this matchup. Maybe it's just the samuses I play, but I think it's always really obvious when they are going to attack. Sometimes I like to empty shorthop approach and they immediately crouch so they can dtilt me. I then use down-b counter to hit them. Be cautious though... you can't be abusing counter too much. You can also predict when they are going to escape your combo if you screw up your spacing. Expect them to nair, so if you have time to pull out a counter, then go for it. I only use counter like 5x per match against samus though. Just keep them guessing.
