First of all, "Estar" is used to express:
1. geographic or physical location: for exemple:
¿Dónde estás? Estoy en el laboratorio.
¿Dónde está Chile? Chile está en América del Sur.
2. state or condition
3. many idiomatic expressions
4. progressive tenses
We can classify your sentence under the first case so that the question will be:
Donde estan mis pantalones?
Sus pantalones estan aqui "OR" Aqui estan sus pantalones
While "Ser" is used to express:
1. the hour, day, and date
2. place of origin
5. religious or political affiliation
6. the material something is made of
8. relationship of one person to another
9. certain impersonal expressions
10. where an event is taking place
11. essential qualities