Writing a paper from Master thesis, but not sure how to organize the paper or what to include in it
You could structure your material as follows. To my perception (at least in computer science) this is more or less standard structure.


Introduction: The bigger picture in which your approach fits in: the problem you are trying to solve. A short description that guides the reader from the more general to the more specific issue.
You could have an extra section regarding some preliminary concepts that are crucial to understanding your work. The nice thing with journals is that you do not have the space restrictions that you have in conferences, and thus you can expand a little.
Related work: Attempts that already exist in the literature, and how you compare with them. Why your solution would be an advance in the state-of-the-art, and under which conditions.
Description of your work: as detailed and as formal you can be regarding e.g. a system architecture, an algorithm, the core idea of the paper.
Performance measurements. A comparison to "competing" approaches in terms of performance.
Optionally, a discussion section, where you discuss about your experiments. This could be merged in the previous section.
Conclusions and future work. A section where you provide your most important findings and give directions towards which your work can be expanded.


Of course, the above are merely indicative and do not apply to all cases. Personally, this is how would start drafting a new journal publication.


  My feeling at the moment is that the paper does not worth the effort.


It is certainly worth the effort. Why not? Even if the idea is not new, your paper would be a study on how your approach performs in certain conditions.

Funny as it may be, this presentation gives some quality advice: http://research.microsoft.com/en-us/um/people/simonpj/papers/giving-a-talk/writing-a-paper-slides.pdf