“Please note that all applications must be accompanied by two letters of recommendation.”

You're going to apply to a school in the U.S. You're reading the rules for applying on the school's website. There's a sentence on the page which says:

Please note that all applications must be accompanied by two letters of recommendation. 

Please note that (sentence)

This is a formal way to direct people's attention to some information. For example, if you're selling something on the internet that has to be mailed, your site might have this sentence:

Please note that delivery may take up to three weeks.

One reason to use "Please note that..." is because it can sometimes seem rude if you say or write things directly without any introduction. For example, if you're making a short introduction at the beginning of a conference, you might announce:

Food and drinks are not allowed in the auditorium.

But that could sound a little too strict. This sounds nicer:

Please note that food and drinks are not allowed in the auditorium.

(something) must be (done)

Use "must" to tell people things that they have to do. "Must" is more formal than "have to" and is also stronger. It gives the impression that you are really serious and won't allow anyone to disobey you. Teachers, politicians, and other authority figures use it a lot. It's also common in written instructions, like in the example above. Another example is:

All reimbursement requests must be submitted by Dec. 8th.

(something is) accompanied by (something)

In the example above, the application must be "accompanied by" two letters of recommendation. That means that the letters have to be included with it. 

The word "accompany" means to go somewhere together with. For example, one of the most common uses of this word is in this sentence: 

All children must be accompanied by an adult.

You can see this on signs at places that are dangerous for kids, like swimming pools.

The word "accompany" is quite formal, so it's mostly used in writing. 

letters of recommendation

When you apply for a school, you often need to get "letters of recommendation". These are letters written by a teacher, boss, coach, or some other authority. They're supposed to be about how great you are. The letters are usually sealed in a closed envelope and sent along with the application.

Letters of recommendation are commonly needed for getting into college, graduate school, getting a scholarship, or for winning certain awards. They're not usually needed in the U.S. for getting most jobs.