Have applied to, and been rejected from, a number of PhD positions; are they really so difficult to get? I am a student who graduated with a Master from a German university in April this year, majored in materials science, willing to further pursue a PHD degree in a European university (or possibly a university in the USA if I can not get anything in the EU). I have already applied to a certain amount of universities´ PHD studentship programs.

I admit that there hardly are positions exactly fitting the thesis work and research activity I had in my Master study program, because materials science is a very diverse and gargantuan subject. Each different university has its own research preference and inclination. Sometimes you may say you can find between 20%-40% overlap with your past experiences, including the similarity of research content, or the techniques being used. So I tried to apply to all of them, the replies were mostly like this: "You can not fit the best of criteria.."  It has been several months, there is still no slight improvement of my application.

My GPA is 3.4/4 (no publications so far), but according to the PhD advertisements I have viewed, some universities have rules about the basic grade requirement you need to have for PhD enrollment, some do not have. The universities I had finished my Master and Bachelor study have certain reputation in their own region or country. My Master degree is Master of science(M.Sc.), Master thesis is about metal-oxide nanostructures synthesis and its application (basically using different approach trying and trying again, compare the final results), on the one hand I am afraid of the simple and even boring thesis work could give people wrong impression about my research experiences that is poor and rudimentary, Professor will have some doubts about whether I am truly quantifying to do some sophisticated PhD work, on the other hand, if I stick to doing metal-oxide fabrication research or related in my PhD study, you need to have solid background in chemistry, which also is what I am lack of. 

Unfortunately I do not have too much contact with my professor (thesis advisor) except having some discusses related to my Master thesis, because our group is very big one and each PhD student is responsible for supervising master students for their thesis work, so Professor could have time and energy doing other things, I only asked my professor for recommendation letter once, maybe I also need his suggestion about my applications.

After I have accepted some rejected letters, I started to think which kind of project could fit my profile, not only I can be accepted by them but I can also enjoy my project and stretch my muscle, doing some useful in materials science field.     

Sometimes I am confounded by various projects and their fancy names offered in the webpages, and do not know what to do next. but I still  have a dream about one day I could leave my fingerprints on the TEM machine and my thoughts on the scientific papers.If you are a PHD student (have successful application experiences) majored in materials science or related area, I kindly ask for suggestion (any suggestion and any opinions will be useful to me).
As for the question in your title (which originally was: "Is it really that difficult finding a funded PHD position?") the answer is it depends on the field and the country. As an engineer, in countries with a well-developed industry, the job opportunities for graduates outside academia are good, thus diminishing the competition for PhD positions. This being said, a grad student is not just hired to lay bricks because there is a wall to be built. It represents a substantial investment for professors who will thus rather have no student than a not-so-good one.

To the point, previous experience in the specific field of the PhD study is almost never a requirement, so I doubt it's the limiting factor in your case. Your grades might be though, or your written english proficiency, but these are guesses.

I think your strategy might be inefficient. From your text it sounds like you sent a large number of applications and are waiting for someone to bite the bait. A personal interaction with people in the labs you are interested in would be a better approach, for example via an internship or a visit, if you can afford it.

So I would narrow it down to a few places where you really would like to work, gather the reasons why you like them, and start establishing a contact via email, say what you like about their approach or research topic and how you think you could fit in. They will then be able to let you know what is needed to be accepted in the graduate program (note that you will still have to comply to the department, university or graduate school requirements in order to be accepted).