present perfect tense and in/on/above.

[Rida*]

In present perdect tense the formution if sentence is,

Subject/helping verb/verb third form/object.

The doctor has treated the patient well. and
The doctor has not treated the patient well. and
Has the doctor not treated the patient well?

But
Can I say,

Has not the doctor treated the patient well?
I mean, can I use "has not" togather in the beginning of the sentence? Will it also be correct , like
Has the doctor not ........?

My second question is, what is the difference?
The pen is on the table.
The pen is above the table.

My third question is.
Birds are making nest in the trees. or
Birds are making nest on the trees.
and
Birds are sitting on the trees. or
Birds are sitting in the tress.

Thank you.

[Esl_Expert]

Hi Rida,
My comments are in blue:

The doctor has treated the patient. OK
The doctor has not treated the patient. OK
Has the doctor treated the patient? This is the question format without negation.

Has the doctor not treated the patient? OK if you want to ask whether "not treated" is true.
Hasn't the doctor treated the patient? This is typically what we would say in spoken English when we need to clarify whether the doctor has or has not treated the patient.
Has not the doctor treated the patient?No, you should only use the contraction of 'has not' to begin this sort of sentence: Hasn't

The pen is on the table. = The pen is in contact with the top/surface of the table.
The pen is above the table. = The pen is not touching the table. It is in a position that is higher than the table. In this sentence, it almost sounds like the pen is floating in the air.

Birds are making nests in the trees.
Birds are making nests on the trees branches.
and
Birds are sitting on the trees. No, generally we would say that they are on the branches.
Birds are sitting in the tress. OK

.
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"It is an affront to treat falsehood with complaisance." Thomas Paine

[Rida*]

Thank you so much.