Which is a better characterization tool to study the surface morphology of material? What other parameters can be studied using these technique? Can we use x-ray instead of electron in case of SEM?
I think SEM is very useful for microstructure analysis, either nature surface or fracture surface. Sometimes, people use it to observe domains in ferroelectrics after chemical etching. There are several modes for SEM machines, such as secondary electron imaging, backscattered electron imaging, and EDX. The latter two are helpful if there is secondary phase in your samples.
SEM is used for surface imaging (primary electrons) and composition analysis (backscatterd electrons). SEM can also be used in analyzing the continuity of the thin film. X-SEM can be used to determine the thickness of the thin film deposited on a substrate. SEM can be used to study surface properties upto nano-scale.
AFM is used to study surface morphology like roughness of the thin film surface in the micron scale. AFM can also be used to produce 3D graph of the surface.
Morphology is a broad term. You would do well to divide it in to its various components, such as roughness, topography, lateral periodicity of features, lateral sizes of features, or height/depth of features. The "better" method will then be the one that works most effectively to obtain the specific value of interest. As an example, SEM only images in 2-D. Based on this, what morphological values cannot be measured by SEM?
Otherwise, I recommend that you read review articles on SEM and AFM to help answer your last two questions.
Of course X-ray microscopy is also feasible - it depends on many factors I guess. The most important is maybe the scale on what you are looking. With AFM, you are restricted to the possible maximum scan size of your instrument, which is in the order of 100 muem typically, and you are able to visualize and quantify features of several Angstroem in size. Again, depending on your instrument, sub-nm features in z-direction are possible, while lateral atomic resolution is difficult, but possible on some instruments. With SEM in combination with a field emitter as electron source, you can not reach these scales, you will need TEM for an atomic resolution. But in that case, you need some special sample preparation, which you will not need for SEM and AFM. So the story is not that simple to tell, and it depends on your samples, and what you will get out from such an analysis.
For roughness, topography, lateral periodicity of features, lateral sizes of features, or height/depth of features, thickness, AFM is very useful technique.....
For, surface images, composition of the surface film, SEM-EDX is very useful technique....
There are good and fundamental information in the link below which is useful for others equipment as well . I know my answer is too late but when somebody search on the benefits of SEM, this question will appear for him. regards