The major difference is lie in their full name, in FESEM , scanning electron microscopy is used while in TEM it is transmission electron. Former can give you grain size, grain-interface morphology, does not require grid as in later. TEM can give you the particle size of powder. So basically the two are different technique and used in different way and purpose.
However, only TEM is not much useful for crystal lattice and defect analysis. It is possible through HRTEM image and SAED pattern. Obviously, a picture image typically in the case of nano-particles (where morphological study is important), will better than indirect calculation(XRD).
Perhaps my following work can explain a bit, (if you need more than please don't hesitate)
Defect induced weak ferroelectricity and magnetism in cubic off-stoichiometric nano bismuth iron garnet: effect of milling duration PK Jha, PA Jha, P Kumar, K Asokan, RK Dwivedi Journal of Materials Science: Materials in Electronics, 1-9, February 2014, Journal of Materials Science Materials in Electronics 25(2) DOI10.1007/s10854-013-1628-x
I think main difference is the following: TEM is used for very thin samples electrons can transmit through (i.e. nanoparticles) to reach the sensor that creates the image, usually very accurate way to see nano-whatever's size in 2D. In contrast, an FESEM can be used to study the morphology of anything of nano/micro scale (i.e. structures, thin film thickness, devices, nanoparticles) since its sensor is positioned to register the emitted secondary electrons -not transmitted or primary ones.
And Yes, TEM is great for lattice defects etc. I think TEM can provide great detail for 2D analysis and XRD can give an idea of the same in 3D. If we assume that 3D is composed many layers of 2D like in the case of crystals, I believe TEM is a better proof than XRD to show lattice defects and determine size.
Both SEM (scanning electron microscope/microscopy) and TEM (transmission electron microscope/microscopy) refer both to the instrument and the method used in electron microscopy.
There are a variety of similarities between the two. Both are types of electron microscopes and give the possibility of seeing, studying, and examining small, subatomic particles or compositions of a sample. Both also use electrons (specifically, electron beams), the negative charge of an atom. Also, both samples in use are required to be “stained” or mixed with a particular element in order to produce images. Images produced from these instruments are highly magnified and have a high resolution.
However, an SEM and TEM also share some differences. The method used in SEM is based on scattered electrons while TEM is based on transmitted electrons. The scattered electrons in SEM are classified as backscattered or secondary electrons. However, there is no other classification of electrons in TEM.
The scattered electrons in SEM produced the image of the sample after the microscope collects and counts the scattered electrons. In TEM, electrons are directly pointed toward the sample. The electrons that pass through the sample are the parts that are illuminated in the image.
The focus of analysis is also different. SEM focuses on the sample’s surface and its composition. On the other hand, TEM seeks to see what is inside or beyond the surface. SEM also shows the sample bit by bit while TEM shows the sample as a whole. SEM also provides a three-dimensional image while TEM delivers a two-dimensional picture.
Agreeing with the above. TEM and more FETEM will give you local "imaging". Structure however must be derived from diffraction modes , either using Xrays or electron beams. In particular ebeams may create deffects more than XRAY, not only find them. And also redox processes