Meaningful output of FIR filter output
If it's a linear phase FIR filter, then the inputs signals will be shifted (delayed) by an amount of group delay at the output.

For a linear phase FIR filter of length $L = 2K+1$ the group delay will be $N = K$ samples. For even length $L = 2K$ FIR filters it will be at $N = (L-1)/2$ ; half-sample position.

For non-linear phase FIR filters, group delay will be dependent on the specific frequency of the applied input signals.  It should be computed from

$$ \tau = - \frac{d \phi(\omega)}{d\omega} $$

where $\phi(\omega)$ is the phase response of the filter. 

The matlab function filter(b,a,x) computes all the samples begining up to input signal length. So the first samples are transients.