Neem alleen medicijnen in die de arts voorschrijft.

Because the full verb is innemen, which is a separable verb in Dutch. In a main clause or an imperative, the first part stays with the verb stem and the prefix moves to the end:

• infinitive: innemen
• imperative: Neem ... in
• statement: Ik neem medicijnen in

This verb means to take in the sense of taking medicine.

So Neem alleen medicijnen in is literally structured like Take only medicines in, but in natural English it means Only take medicines ...

Neem is the basic imperative form, used for giving an instruction or command.

It is based on the verb nemen:

• infinitive: nemen
• stem: neem
• imperative: Neem!

A more formal version with u is often:

• Neemt u alleen medicijnen in die de arts voorschrijft.

So Neem here is the plain command form, often used in instructions, warnings, or general advice.

Alleen means only here.

It modifies medicijnen in the sense of:

• Only take medicines that the doctor prescribes

So the idea is not just take medicines, but take only those medicines that meet the condition in the relative clause.

Dutch often places alleen before the noun or phrase it limits:

• Neem alleen medicijnen in ... = Take only medicines ...

Yes, this is a common thing learners notice. Dutch often uses medicijnen in the plural where English might use medication as an uncountable noun.

So:

• medicijnen = medicines / medication

In this sentence, the plural sounds very natural because it refers to any medicine(s) a person might take. Dutch can also use words like medicatie, but medicijnen is very common and everyday.

It is a relative clause. It gives extra information about medicijnen.

So:

• medicijnen = medicines
• die de arts voorschrijft = that the doctor prescribes

Together:

• medicijnen die de arts voorschrijft = medicines that the doctor prescribes

This clause tells you which medicines are meant: not any medicines, only the ones prescribed by the doctor.

Because die refers here to medicijnen, which is plural.

In Dutch relative clauses:

• plural nouns take die
• singular de-words usually take die
• singular het-words usually take dat

Examples:

• de man die ...
• het boek dat ...
• de medicijnen die ...
• de medicijnen is plural, so die is the correct choice.

Because die de arts voorschrijft is a subordinate clause (specifically a relative clause), and in Dutch subordinate clauses the verb normally goes to the end.

Compare:

• main clause: De arts schrijft medicijnen voor.
• relative clause: ... medicijnen die de arts voorschrijft

Also, voorschrijven is another separable verb:

• main clause: schrijft ... voor
• subordinate clause: voorschrijft

So in the relative clause, the two parts come back together and the whole verb goes to the end.

De arts here is being used in a generic sense: the doctor as a category, not necessarily one specific doctor already mentioned in the conversation.

Dutch often uses de + singular noun to talk about a role or profession in a general, standard way.

Depending on context, you could also say:

• een arts = a doctor
• uw arts = your doctor

But de arts works very naturally in general medical instructions.

Yes, arts is a de-word, so the correct article is de:

• de arts = the doctor

This is something you mostly just have to learn with the noun. There is no reliable rule from the form alone that will always tell you whether a noun is a de-word or a het-word.

Yes, and that changes the nuance slightly.

• Neem alleen medicijnen in die de arts voorschrijft = Only take medicines that the doctor prescribes.
• Neem alleen de medicijnen in die de arts voorschrijft = Only take the medicines that the doctor prescribes.

Without de, it sounds more general.
With de, it can sound more like a specific set of medicines is being referred to.

Both are grammatical, but the version without de is very natural for general advice.