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We had submitted a manuscript in September 2016. Till now the paper remains with the editor showing status "With Editor".

After several reminders, we could not get any reply from the journal side. Only it was the editorial manager (staff) who responded with standard reply "I have forwarded your mail to the editor...".

Finally (approx. 20 days back), we decided to withdraw the manuscript from the journal and hence we wrote a formal mail to the journal. Till now, we have sent 3 reminders regarding the same and have received no confirmation from the journal side. However, the status of the paper remains the same "With editor".

Question: Now, should we consider the paper has been withdrawn from the journal and submit the paper elsewhere?

I am really inexperienced in such process and suggestions would help me learn it.

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Your question does not contain information necessary to give you the best advice.

One possible interpretation is that you submitted the paper in Sept '16, waited a month and then started sending emails at the rate of about two a month asking about the process of its evaluation. Then not getting an answer, you got impatient and decided just before the winter holidays to withdraw your paper and try for a quicker response elsewhere. Whether or not that is a fair interpretation, I will try to make some comments about the submission and review process that you may find helpful.

First, from an author's point of view, the editorial process of reviewing a paper works at a regrettably slow pace. Often the paper is assigned to an associate editor for a preliminary review, and then sent to several reviewers for their opinion. Typically, associate editors and referees are donating their time and are juggling several projects at once. Time delays vary widely by field, by individual journal, and by submissions to any one journal, but several months is certainly not an unusual delay.

Second, withdrawing a paper after submission is unusual and should not be done without compelling reasons, such as discovery of fatal errors in the paper. As mentioned in @Kimball's link, withdrawal means wasted time by editors and reviewers. It should be done rarely, for compelling reasons, and with abject apologies. Withdrawal because you think the review process is too slow might be OK after very many months without any communication or signs of progress, but not after the relatively short time you describe.

If this is mainly on target, I suggest you stop emailing the publication manager and wait for several months before submitting your paper elsewhere. Meanwhile, spend your energy working on your next paper.

A couple of personal anecdotes may be helpful to understand the time scale. (a) I have served several times on the publications board of a large professional society that publishes several well-known journals in my field. Trying to speed the review process was always a major topic of discussion. We used a high 'clearance rate' by six months as a sign of progress. (b) Recently, by request, I submitted an article for an encyclopedia organized by a major scientific publisher. I received periodic reminders from the publisher's staff and the editor of the due date, which I barely met. Then I heard nothing for four months until referees reports came in, along with requests to make a few changes and additions within a week. None of this surprised me because this was my third invited article for this publisher, and the first two had proceeded on a similar time scale.

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