You have to specify a target for each pod.
e.g. if before you had your Podfile written like this:
pod 'Alamofire', '~> 3.1.4'
pod 'SwiftyJSON', '~> 2.3.2'
just change it to
target "TargetName" do
pod 'Alamofire', '~> 3.1.4'
pod 'SwiftyJSON', '~> 2.3.2'
end