If you know which object is near. You can use Destroy.
Destroy(cloneObject);
If you don't know which objects are near, you can use List to add clone objects
and check it is near.(When you create clone you need to add clone to the list.)
You need to add using System.Collections.Generic;
for using List.
Example code: (It's C# code but you can understand logic)
....
using System.Collections.Generic;
public List<GameObject>cloneObjectList;
private void cloneObject(){
GameObject cloneObject = Instantiate(originalPrefab,position,rotation);
cloneObjectList.add(cloneObject);
}
private void checkDistance(){
foreach(GameObject cloneObject in cloneObjectList){
float distance = Vector3.Distance(Food.transform.position, cloneObject.transform.position);
if(distance <0.3f){
cloneObjectList.Remove(cloneObject);
Destroy(cloneObject);
}
}
}
Moreover you can use Collision detection system.