There is no discounted weighting of freshman year vs later years (as might happen in some college admissions processes). And a 3.49 average is not going to get you into medical school so this needs to change, as you already know.
Here’s the data:
https://www.aamc.org/data/facts/applicantmatriculant/157998/mcat-gpa-grid-by-selected-race-ethnicity.html
How to change it? The most important thing, other than using every academic resource available to you to ensure that you do as well as you possibly can, is not to overload yourself. If you have two pre-req classes, for example, like org chem and bio (with labs), you absolutely do not want even one more demanding class during that semester. You will have plenty of time to finish your medical school pre-reqs, your distribution requirements and your major without piling on the hardest classes all at the same time. It requires planning your schedule ahead for the entire time you are in college, but most pre-meds manage to do this. You can too.
Remember, you still want to have a social life, enough sleep, and time to do things like research, medical volunteering, etc…and it won’t happen if you aren’t carefully thinking through what you plan to take and when so you have some work/life balance. That’s the #1 challenge of pre-meds, medical students and even doctors, everywhere.