Aggregation of nanoparticles is often related to the shape, surface properties and charge contained in them... a reading on Derjaguin-Landau-Verwey-Overbeak and Extended Derjaguin-Landau-Verwey-Overbeak theory of aggregation could provide some insights...

Grafting of ligands on the surfaces may prevent aggregation. I

I agreed. Grafting using peptide or short ligands ( watch the functional group) way to go.

Suspending nanparticles in sucrose solution (1 to 10 %) (or other sugars such as trehalose) can help prevent aggregation. 

Once aggregated, depending on the nature and type of your nanoparticles, it can be bring back to non-aggregated stage by sonication. 

Thank you Vivek Sir, that was helpful.

good answers from vivek sir and Radhamanohar sir.

Select a suitable capping agent for nanoparticle and go for probe based ultrasonication.  

To totally prevent the aggregation or agglomeration of nanoparticles is rather difficult due to their small size and mainly attractive forces between. Milling by attrition in organic medium is well known way to decrease the factor of agglomeration. Ultrasonic treatment can temporary decrease the aggregation, however after very short time , the situation can be the same as it was before ultrarsonic treatment.

I've dealt with polymer-GO aggregation and you can consult these two papers, where re-aggregation is avoided by different methods.

Article A novel approach to prevent graphene oxide re-aggregation du...

Article A green method to prepare nanosilica modified graphene oxide...