Samus will most likely be spamming crouch cancel and down smash, so you should make it a priority to never do a falling aerial into a Samus that is crouching. Your biggest advantage in this matchup is the length of your sword. Perfectly spaced fairs (hitting with the very tip of the sword) can beat most of Samus's aerial options, giving her virtually no aerial game against Marth. IIRC, a perfectly spaced fair can also hit and explode a missle without you taking any damage, and this is not all that hard to learn.
Samus' weight and fall speed make her an incredibly hard character to combo. You might be able to fthrow>fair chain into a Ken combo at low percents if they DI into you, but in general you will not be doing lengthy combos against Samus. Instead you should focus on getting her in the air or off the stage, and then repeatedly repelling her attempts to get back on stage. Once you have samus either in the air or off stage you do not have to be in a hurry because you already have a huge advantage. The number 1 mistake I see when people play Vs Samus is that players often get impatient and go for crazy offstage kill attempts when they could have just hit her back off again with a simple move. You gotta be prepared for Samus to live a long time, and you have to respect the screw attack. Screw attack can completely reverse a situation in Samus's favor, especially offstage. When Samus is off stage you have to remember that screw attack is an offensive option that can easily screw you over.
Mastering down air is incredibly useful vs Samus, as you can intercept screw attack with dair. Having that skill makes it significantly more difficult for Samus to recover. If Samus is off stage, you should be constantly thinking about ways you can dair her. In many cases you can do an onstage SHFFL dair at the edge of the stage and catch her as she rises toward the stage. This works because the sword hitbox actually goes through the stage.
Samus' best tool against Marth is wavedash OoS movement. Since she has a weak aerial game, she has to stay grounded to do most of her work. Samus finds openings by shielding a sword move, then wavedashing towards you and doing a move (most likely downsmash, but fsmash and ftilt are also used). If Samus feels pressured in shield she may screw attack to escape the situation. As Marth, if you are spacing correctly you should not be getting hit by screw attack OoS.
Lastly, perhaps the most pivotal aspect of this matchup is the fact that Samus's grab is terrible and is almost never used. Samus has basically no grab game, meaning that you can shield all day and never fear getting grabbed. This is great in neutral for baiting out moves. Try it out. When you get close to a Samus in neutral just shield an 9 times out of 10 they will do attacks rather than grabbing. This is because the grab is so slow that players can actually jest react to it with spot dodge, and then they get a free punish. Even if Samus gets a grab there's not that much she can do with it. So if you can get your shield up against Samus, you will very often find a free shield grab. Some Samuses have responded to this kind of shielding by spamming spot dodge (Samus's spot dodge is great) and then looking for an opportunity to downsmash you after your shield depletes a little bit (downsmash hits your feet after shield shrinks a bit). So the proper response to that is to light shield and angle the shield downward to cover your feet. That way Samus has basically no good options, and if she down smashes you will be pushed away to safety because you are light shielding.