flowHash = {'hola':{'wassup':{'bleh':9000, 'hi':9000}}}
sip = 'hola'
dip = 'wassup'
dport = 90
otherHash = {}

for sips in flowHash: #se itera por todos los dip y sus counters o puertos
    for dips, dports in flowHash[sips].items():
        if len(dports) >= 1: #si la cantidad de puertos es mayor o igual a 100, nos interesan
                                #y por lo tanto se guardan en un hash
            print len(dports)
            if sips in otherHash:
                otherHash[sips][dips] = dports

            else:
                otherHash[sips] = {dips: dports}

print otherHash