Segregate scat into different components i.e plant matter, insects etc and determine weight and volume of these different components. Then identify dietary components...plants through cell shapes observed by using microscope and for insects contact antamologist. 

What type of reptile and what type of analysis? Many lizards are going to be consuming different items from snakes, for example. Emydid turtles vs. crocodilian is another contrast.  

I may be of assistance with regards to DNA analysis of fecal samples. Please inform if this is something you are considering.

I have experience in analyzing / identification invertebrates from dissected stomachs of Madagascan tortoises (worked for Durrell's Fund many years ago). In many cases it is possible to identify even species of invertebrates from reptile stomachs. Of course, it depends on the species and its diet. I am quite sure it can be very hard to identify stomach content, for example, of Chamaeleolis lizards as theirs jaws are very strong and all invertebrates just getting squashed / chewed completely. On the other hand, you always know the main food source for Chamaeleolis are land snails :)

So in fact it strongly depends which species / species group are you going to analyze and what is the main diet of this species / group, as well as fresh stomach samples or excrement are.

@Dimitry Telnov

@Mark Spangler

@Gordon W Schuett

@Faraz Akrim

Thanks for sparing your valuable time for replying. Actually am planning to work out on the fecal samples of re-introduced Crocodiles to understand their diet in a semi-arid landscape. Since, I am getting good number of fecal samples of the considered species, I guess it will help out to be an important step in understanding their diet.

Is the fecal sample analysis is the same as we do for the carnivores or it some thing different?

I will be obliged with your comments.