אחרי שאני סורקת את התעודה, אני שומרת עותק אחד במחשב ועותק אחד בתיק.

Because the speaker is female.

In Hebrew, present-tense verb forms agree with the subject in gender and number. With אני (I), you still have to choose a masculine or feminine form:

• אני סורקת / אני שומרת = a woman is speaking
• אני סורק / אני שומר = a man is speaking

So if a male speaker said the same sentence, it would be:

אחרי שאני סורק את התעודה, אני שומר עותק אחד במחשב ועותק אחד בתיק.

It means after I...

This structure is made of:

• אחרי = after
• ש־ = that / when / which introduces a clause
• אני = I

So אחרי שאני סורקת is literally something like after that I scan, but in natural English it is simply after I scan.

This is a very common Hebrew pattern.

Because Hebrew often uses the present form for habitual actions, instructions, or steps in a process.

So:

• אחרי שאני סורקת את התעודה, אני שומרת...
  = after I scan the document, I save...

This sounds natural when describing what one usually does or what happens in a sequence.

A different version is also possible:

• אחרי שסרקתי את התעודה, שמרתי...
  = after I scanned the document, I saved...

That version sounds more like a specific completed past event.
The sentence you were given sounds more like a routine or procedure.

את is the marker of a definite direct object.

It does not mean you here.
It has no direct English equivalent.

Hebrew uses את before a direct object that is definite, such as:

• a noun with ה־
• a proper name
• a pronoun

So:

• סורקת את התעודה = scans the document/certificate

But Hebrew normally does not use את before an indefinite direct object, which is why you do not see it before עותק אחד.

Because עותק אחד is indefinite: it means one copy, not the copy.

Hebrew usually uses את only with definite direct objects.

Compare:

• אני סורקת את התעודה = I scan the document
• אני שומרת עותק אחד = I save one copy

If the object were definite, then את could appear:

• אני שומרת את העותק = I save the copy

In Hebrew, the number one usually comes after the singular noun.

So:

• עותק אחד = one copy
• מסמך אחד = one document
• תמונה אחת = one picture

Also, the number must agree in gender with the noun:

• עותק is masculine, so: אחד
• a feminine noun would take אחת

That is why it is עותק אחד.

ב־ is a very flexible preposition. It can mean in, on, at, or sometimes something similar, depending on context.

So:

• במחשב can mean something like on the computer or in the computer
• בתיק can mean in the bag, in the folder, or in the file, depending on what תיק means in context

English often makes finer distinctions than Hebrew here. Hebrew is comfortable using ב־ in places where English might choose different prepositions.

Because the sentence has two clauses, and repeating אני makes the subject clear.

Hebrew often repeats the subject in this kind of structure, especially in the present tense, because present-tense forms do not clearly show person the way past and future forms do.

For example, שומרת tells you:

• feminine
• singular

but not by itself whether the subject is I, you, or she.
So אני helps make it explicit.

That is why אני שומרת is very natural here.

Yes. Hebrew could also say:

אחרי שאני סורקת את התעודה, אני שומרת עותק אחד במחשב ואחד בתיק.

That means the same thing.

The full version with עותק אחד repeated is just more explicit and balanced:

• עותק אחד במחשב
• עותק אחד בתיק

Both are natural.

Yes, it is very normal.

The sentence follows a common pattern:

1. time clause first
   אחרי שאני סורקת את התעודה
2. main clause next
   אני שומרת עותק אחד במחשב ועותק אחד בתיק

This is a very standard way to describe a sequence of actions in Hebrew.

You could sometimes rearrange parts for emphasis, but the version you have is straightforward and natural.