The 5 steps to make this change are easy.
1) List what business applications you want to monitor? Ask yourself: Do I want to measure performance to Cloud services such as salesforce.com, Skype or in house applications such as SAP?
2) Decide what metrics you want to export. FnF can export MAC addresses, VLAN details and depending on the hardware, you can export entire packets, Cisco TrustSec, CoS, Jitter, packet loss, TCP latency, NAT details, NBAR, IP SLA, etc. Make sure your NetFlow Analyzer can filter and report on these details else, by our NetFlow collector!

3) Make sure you are running the proper IOS version. Cisco IOS 15.2(2)T or more recent for the most capable Flexible NetFlow exports which combine Cisco NBAR and Cisco Medianet Performance Monitoring.
4) Telnet to the router and disable traditional NetFlow and remove all of the commands from the router. Now try to forget about how to setup NetFlow. Commands like ip route-cache flow aren’t going to work anymore.
5) Then, just setup Flexible NetFlow
Keep in mind that performing step 5 and configuring flexible netflow prior to step 4 will cause some duplicate flow exports. This is not something you want as it will over state utilization in the NetFlow reporting and it can also potentially cause problems for network security monitoring. Either way, it’s really a simple process and a huge value add to your overall network monitoring efforts. Don't forget to setup the new Cisco Performance Routing Flexible NetFlow exports. Call us if you need help.
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