1/2 Day Trips From Prague
 

So we will be in Prague in mid-March and have looked into a couple of side trips to both Plzen and Kutna Hora. I have seen several "tours" thru various companies, but they all seem to begin in late morning or early afternoon which cuts into the day in Prague (only there 3 days). Is it possible to do these on our own -- take a bus or train and visit on our on timeframe? Thinking of leaving early a.m. in order to be back to the city by at least 2 or 3 p.m. If so, what would be best station to travel from to get to both as we are staying close to Prague Castle. Thanks.

Yes. Take a look at the schedules on the Czech railway site, Ceske Drahy. https://www.cd.cz/en/default.htm

Trains run regularly to Kutna Hora with a travel time of about an hour. The walk from the Kutna Hora Main Station to the Ossuary is about 20 minutes; and the walk from the Kuntna Hora Mesto Station to St. Barbara's is also about the same. Walking between the two, however, would take about an hour. To find bus connections between the Kutná Hora train station, Sedlec Ossuary, and city center, go to Jizdnirady.cz and choose "Kutna Hora Public Transport" in the "Timetable" drop-down. For the form to work, you'll have to type in the exact Czech names (with accents) of the bus stops.

main train station - hl.nádr.
bus station - aut.st.
city center - Centrum
Sedlec Ossuary - Sedlec,Tabák
St. Barbara's - Kutná Hora, k nem

Prague to Plzen takes about 90 minutes. Pilzen is much larger, and has trams and buses to make moving around easier.
Public transportation in Pilsen: Official website of the City of Pilsen

I hope this is helpful.

Plzen is a bit to far for a half day trip.over 90 minutes each way by train and if you want to do a tour of the brewery you need around 90 minutes for that.
Kutna Hora is possible with an early start but the main sites are a bit spread out ie the Bone church is a bout 2,5 kilometres from the main town which is set on quite a steep hill.main train station is 3 Kilometeres from the main town though there is a small local train gets you closer but you still have the hill.
You could go to karlstejn castle, about 40 minutes by train from Prague,about a 15-20 minute walk up to the castle and it is a nice place.best to book a tour before hand ,you can get into the main courtyard without going on a tour and it is pretty good with some good views. I often go walking in the area.The place is closed on a Monday can't even get access to the courtyard on a Monday.

In addition to Fourfortravel's post there is a mini bus that runs from the Ossuary to St Barbara's but runs only when there is enough people to do so minimum of 3 people,ask in the ossuary about this.